Starting phenix.real_space_refine on Sat Feb 24 17:53:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kln_22917/02_2024/7kln_22917.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.548 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 28776 2.51 5 N 7644 2.21 5 O 8964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ARG 110": "NH1" <-> "NH2" Residue "A1 ASP 135": "OD1" <-> "OD2" Residue "A1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 171": "OE1" <-> "OE2" Residue "A1 ASP 174": "OD1" <-> "OD2" Residue "A1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 182": "OE1" <-> "OE2" Residue "A1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ASP 193": "OD1" <-> "OD2" Residue "A1 GLU 205": "OE1" <-> "OE2" Residue "A1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 GLU 237": "OE1" <-> "OE2" Residue "A1 GLU 289": "OE1" <-> "OE2" Residue "A1 ARG 302": "NH1" <-> "NH2" Residue "A1 GLU 310": "OE1" <-> "OE2" Residue "A1 GLU 318": "OE1" <-> "OE2" Residue "A1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ARG 110": "NH1" <-> "NH2" Residue "B1 ASP 135": "OD1" <-> "OD2" Residue "B1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 171": "OE1" <-> "OE2" Residue "B1 ASP 174": "OD1" <-> "OD2" Residue "B1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 182": "OE1" <-> "OE2" Residue "B1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 193": "OD1" <-> "OD2" Residue "B1 GLU 205": "OE1" <-> "OE2" Residue "B1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 GLU 237": "OE1" <-> "OE2" Residue "B1 GLU 289": "OE1" <-> "OE2" Residue "B1 ARG 302": "NH1" <-> "NH2" Residue "B1 GLU 310": "OE1" <-> "OE2" Residue "B1 GLU 318": "OE1" <-> "OE2" Residue "B1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ARG 110": "NH1" <-> "NH2" Residue "C1 ASP 135": "OD1" <-> "OD2" Residue "C1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 171": "OE1" <-> "OE2" Residue "C1 ASP 174": "OD1" <-> "OD2" Residue "C1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 182": "OE1" <-> "OE2" Residue "C1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ASP 193": "OD1" <-> "OD2" Residue "C1 GLU 205": "OE1" <-> "OE2" Residue "C1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 237": "OE1" <-> "OE2" Residue "C1 GLU 289": "OE1" <-> "OE2" Residue "C1 ARG 302": "NH1" <-> "NH2" Residue "C1 GLU 310": "OE1" <-> "OE2" Residue "C1 GLU 318": "OE1" <-> "OE2" Residue "C1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 110": "NH1" <-> "NH2" Residue "D1 ASP 135": "OD1" <-> "OD2" Residue "D1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 171": "OE1" <-> "OE2" Residue "D1 ASP 174": "OD1" <-> "OD2" Residue "D1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 182": "OE1" <-> "OE2" Residue "D1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ASP 193": "OD1" <-> "OD2" Residue "D1 GLU 205": "OE1" <-> "OE2" Residue "D1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 237": "OE1" <-> "OE2" Residue "D1 GLU 289": "OE1" <-> "OE2" Residue "D1 ARG 302": "NH1" <-> "NH2" Residue "D1 GLU 310": "OE1" <-> "OE2" Residue "D1 GLU 318": "OE1" <-> "OE2" Residue "D1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 ARG 110": "NH1" <-> "NH2" Residue "E1 ASP 135": "OD1" <-> "OD2" Residue "E1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 GLU 171": "OE1" <-> "OE2" Residue "E1 ASP 174": "OD1" <-> "OD2" Residue "E1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 GLU 182": "OE1" <-> "OE2" Residue "E1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 ASP 193": "OD1" <-> "OD2" Residue "E1 GLU 205": "OE1" <-> "OE2" Residue "E1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E1 GLU 237": "OE1" <-> "OE2" Residue "E1 GLU 289": "OE1" <-> "OE2" Residue "E1 ARG 302": "NH1" <-> "NH2" Residue "E1 GLU 310": "OE1" <-> "OE2" Residue "E1 GLU 318": "OE1" <-> "OE2" Residue "E1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 ARG 110": "NH1" <-> "NH2" Residue "F1 ASP 135": "OD1" <-> "OD2" Residue "F1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 171": "OE1" <-> "OE2" Residue "F1 ASP 174": "OD1" <-> "OD2" Residue "F1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 182": "OE1" <-> "OE2" Residue "F1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 ASP 193": "OD1" <-> "OD2" Residue "F1 GLU 205": "OE1" <-> "OE2" Residue "F1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 237": "OE1" <-> "OE2" Residue "F1 GLU 289": "OE1" <-> "OE2" Residue "F1 ARG 302": "NH1" <-> "NH2" Residue "F1 GLU 310": "OE1" <-> "OE2" Residue "F1 GLU 318": "OE1" <-> "OE2" Residue "F1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 ARG 110": "NH1" <-> "NH2" Residue "G1 ASP 135": "OD1" <-> "OD2" Residue "G1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 GLU 171": "OE1" <-> "OE2" Residue "G1 ASP 174": "OD1" <-> "OD2" Residue "G1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 GLU 182": "OE1" <-> "OE2" Residue "G1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 ASP 193": "OD1" <-> "OD2" Residue "G1 GLU 205": "OE1" <-> "OE2" Residue "G1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G1 GLU 237": "OE1" <-> "OE2" Residue "G1 GLU 289": "OE1" <-> "OE2" Residue "G1 ARG 302": "NH1" <-> "NH2" Residue "G1 GLU 310": "OE1" <-> "OE2" Residue "G1 GLU 318": "OE1" <-> "OE2" Residue "G1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 ARG 110": "NH1" <-> "NH2" Residue "H1 ASP 135": "OD1" <-> "OD2" Residue "H1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 GLU 171": "OE1" <-> "OE2" Residue "H1 ASP 174": "OD1" <-> "OD2" Residue "H1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 GLU 182": "OE1" <-> "OE2" Residue "H1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 ASP 193": "OD1" <-> "OD2" Residue "H1 GLU 205": "OE1" <-> "OE2" Residue "H1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H1 GLU 237": "OE1" <-> "OE2" Residue "H1 GLU 289": "OE1" <-> "OE2" Residue "H1 ARG 302": "NH1" <-> "NH2" Residue "H1 GLU 310": "OE1" <-> "OE2" Residue "H1 GLU 318": "OE1" <-> "OE2" Residue "H1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 ARG 110": "NH1" <-> "NH2" Residue "I1 ASP 135": "OD1" <-> "OD2" Residue "I1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 GLU 171": "OE1" <-> "OE2" Residue "I1 ASP 174": "OD1" <-> "OD2" Residue "I1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 GLU 182": "OE1" <-> "OE2" Residue "I1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 ASP 193": "OD1" <-> "OD2" Residue "I1 GLU 205": "OE1" <-> "OE2" Residue "I1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I1 GLU 237": "OE1" <-> "OE2" Residue "I1 GLU 289": "OE1" <-> "OE2" Residue "I1 ARG 302": "NH1" <-> "NH2" Residue "I1 GLU 310": "OE1" <-> "OE2" Residue "I1 GLU 318": "OE1" <-> "OE2" Residue "I1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 ARG 110": "NH1" <-> "NH2" Residue "J1 ASP 135": "OD1" <-> "OD2" Residue "J1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 GLU 171": "OE1" <-> "OE2" Residue "J1 ASP 174": "OD1" <-> "OD2" Residue "J1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 GLU 182": "OE1" <-> "OE2" Residue "J1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 ASP 193": "OD1" <-> "OD2" Residue "J1 GLU 205": "OE1" <-> "OE2" Residue "J1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J1 GLU 237": "OE1" <-> "OE2" Residue "J1 GLU 289": "OE1" <-> "OE2" Residue "J1 ARG 302": "NH1" <-> "NH2" Residue "J1 GLU 310": "OE1" <-> "OE2" Residue "J1 GLU 318": "OE1" <-> "OE2" Residue "J1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 ARG 110": "NH1" <-> "NH2" Residue "K1 ASP 135": "OD1" <-> "OD2" Residue "K1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 GLU 171": "OE1" <-> "OE2" Residue "K1 ASP 174": "OD1" <-> "OD2" Residue "K1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 GLU 182": "OE1" <-> "OE2" Residue "K1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 ASP 193": "OD1" <-> "OD2" Residue "K1 GLU 205": "OE1" <-> "OE2" Residue "K1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K1 GLU 237": "OE1" <-> "OE2" Residue "K1 GLU 289": "OE1" <-> "OE2" Residue "K1 ARG 302": "NH1" <-> "NH2" Residue "K1 GLU 310": "OE1" <-> "OE2" Residue "K1 GLU 318": "OE1" <-> "OE2" Residue "K1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 ARG 110": "NH1" <-> "NH2" Residue "L1 ASP 135": "OD1" <-> "OD2" Residue "L1 PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 GLU 171": "OE1" <-> "OE2" Residue "L1 ASP 174": "OD1" <-> "OD2" Residue "L1 TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 GLU 182": "OE1" <-> "OE2" Residue "L1 PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 ASP 193": "OD1" <-> "OD2" Residue "L1 GLU 205": "OE1" <-> "OE2" Residue "L1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L1 GLU 237": "OE1" <-> "OE2" Residue "L1 GLU 289": "OE1" <-> "OE2" Residue "L1 ARG 302": "NH1" <-> "NH2" Residue "L1 GLU 310": "OE1" <-> "OE2" Residue "L1 GLU 318": "OE1" <-> "OE2" Residue "L1 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ASP 5": "OD1" <-> "OD2" Residue "A2 GLU 27": "OE1" <-> "OE2" Residue "A2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 GLU 65": "OE1" <-> "OE2" Residue "A2 ASP 91": "OD1" <-> "OD2" Residue "A2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 5": "OD1" <-> "OD2" Residue "B2 GLU 27": "OE1" <-> "OE2" Residue "B2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 65": "OE1" <-> "OE2" Residue "B2 ASP 91": "OD1" <-> "OD2" Residue "B2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ASP 5": "OD1" <-> "OD2" Residue "C2 GLU 27": "OE1" <-> "OE2" Residue "C2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 65": "OE1" <-> "OE2" Residue "C2 ASP 91": "OD1" <-> "OD2" Residue "C2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ASP 5": "OD1" <-> "OD2" Residue "D2 GLU 27": "OE1" <-> "OE2" Residue "D2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 GLU 65": "OE1" <-> "OE2" Residue "D2 ASP 91": "OD1" <-> "OD2" Residue "D2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 ASP 5": "OD1" <-> "OD2" Residue "E2 GLU 27": "OE1" <-> "OE2" Residue "E2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 GLU 65": "OE1" <-> "OE2" Residue "E2 ASP 91": "OD1" <-> "OD2" Residue "E2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 ASP 5": "OD1" <-> "OD2" Residue "F2 GLU 27": "OE1" <-> "OE2" Residue "F2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 65": "OE1" <-> "OE2" Residue "F2 ASP 91": "OD1" <-> "OD2" Residue "F2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 ASP 5": "OD1" <-> "OD2" Residue "G2 GLU 27": "OE1" <-> "OE2" Residue "G2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 GLU 65": "OE1" <-> "OE2" Residue "G2 ASP 91": "OD1" <-> "OD2" Residue "G2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 ASP 5": "OD1" <-> "OD2" Residue "H2 GLU 27": "OE1" <-> "OE2" Residue "H2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 GLU 65": "OE1" <-> "OE2" Residue "H2 ASP 91": "OD1" <-> "OD2" Residue "H2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I2 ASP 5": "OD1" <-> "OD2" Residue "I2 GLU 27": "OE1" <-> "OE2" Residue "I2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I2 GLU 65": "OE1" <-> "OE2" Residue "I2 ASP 91": "OD1" <-> "OD2" Residue "I2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J2 ASP 5": "OD1" <-> "OD2" Residue "J2 GLU 27": "OE1" <-> "OE2" Residue "J2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J2 GLU 65": "OE1" <-> "OE2" Residue "J2 ASP 91": "OD1" <-> "OD2" Residue "J2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 ASP 5": "OD1" <-> "OD2" Residue "K2 GLU 27": "OE1" <-> "OE2" Residue "K2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 GLU 65": "OE1" <-> "OE2" Residue "K2 ASP 91": "OD1" <-> "OD2" Residue "K2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 ASP 5": "OD1" <-> "OD2" Residue "L2 GLU 27": "OE1" <-> "OE2" Residue "L2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 GLU 65": "OE1" <-> "OE2" Residue "L2 ASP 91": "OD1" <-> "OD2" Residue "L2 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45564 Number of models: 1 Model: "" Number of chains: 24 Chain: "A1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "B1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "C1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "D1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "E1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "F1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "G1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "H1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "I1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "J1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "K1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "L1" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2902 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 7, 'TRANS': 353} Chain breaks: 1 Chain: "A2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "E2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "J2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L2" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 895 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Time building chain proxies: 21.30, per 1000 atoms: 0.47 Number of scatterers: 45564 At special positions: 0 Unit cell: (159.57, 159.57, 153.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 8964 8.00 N 7644 7.00 C 28776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYSA2 32 " - pdb=" SG CYSB2 42 " distance=2.12 Simple disulfide: pdb=" SG CYSA2 42 " - pdb=" SG CYSL2 32 " distance=1.94 Simple disulfide: pdb=" SG CYSB2 32 " - pdb=" SG CYSC2 42 " distance=2.05 Simple disulfide: pdb=" SG CYSC2 32 " - pdb=" SG CYSD2 42 " distance=2.00 Simple disulfide: pdb=" SG CYSD2 32 " - pdb=" SG CYSE2 42 " distance=2.15 Simple disulfide: pdb=" SG CYSE2 32 " - pdb=" SG CYSF2 42 " distance=2.04 Simple disulfide: pdb=" SG CYSF2 32 " - pdb=" SG CYSG2 42 " distance=2.02 Simple disulfide: pdb=" SG CYSG2 32 " - pdb=" SG CYSH2 42 " distance=1.99 Simple disulfide: pdb=" SG CYSH2 32 " - pdb=" SG CYSI2 42 " distance=2.01 Simple disulfide: pdb=" SG CYSI2 32 " - pdb=" SG CYSJ2 42 " distance=2.14 Simple disulfide: pdb=" SG CYSJ2 32 " - pdb=" SG CYSK2 42 " distance=1.96 Simple disulfide: pdb=" SG CYSK2 32 " - pdb=" SG CYSL2 42 " distance=1.93 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.64 Conformation dependent library (CDL) restraints added in 7.2 seconds 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10632 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 49 sheets defined 52.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGA1 18 " --> pdb=" O LEUA1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNA1 19 " --> pdb=" O ILEA1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'A1' and resid 14 through 19' Processing helix chain 'A1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRA1 40 " --> pdb=" O META1 36 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 58 Processing helix chain 'A1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSA1 74 " --> pdb=" O GLUA1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGA1 75 " --> pdb=" O ILEA1 71 " (cutoff:3.500A) Processing helix chain 'A1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSA1 81 " --> pdb=" O SERA1 77 " (cutoff:3.500A) Processing helix chain 'A1' and resid 168 through 176 Proline residue: A1 173 - end of helix Processing helix chain 'A1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUA1 188 " --> pdb=" O GLUA1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNA1 189 " --> pdb=" O LEUA1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEA1 191 " --> pdb=" O TYRA1 187 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASNA1 192 " --> pdb=" O GLUA1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERA1 202 " --> pdb=" O ARGA1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEA1 204 " --> pdb=" O SERA1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUA1 205 " --> pdb=" O GLYA1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSA1 206 " --> pdb=" O SERA1 202 " (cutoff:3.500A) Processing helix chain 'A1' and resid 216 through 223 Processing helix chain 'A1' and resid 226 through 238 removed outlier: 3.527A pdb=" N ILEA1 230 " --> pdb=" O GLUA1 226 " (cutoff:3.500A) Processing helix chain 'A1' and resid 263 through 280 Processing helix chain 'A1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUA1 286 " --> pdb=" O GLYA1 282 " (cutoff:3.500A) Processing helix chain 'A1' and resid 301 through 304 Processing helix chain 'A1' and resid 305 through 314 Processing helix chain 'A1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEA1 328 " --> pdb=" O LEUA1 324 " (cutoff:3.500A) Processing helix chain 'A1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSA1 352 " --> pdb=" O GLUA1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAA1 353 " --> pdb=" O TYRA1 349 " (cutoff:3.500A) Processing helix chain 'A1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSA1 372 " --> pdb=" O ALAA1 369 " (cutoff:3.500A) Processing helix chain 'B1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGB1 18 " --> pdb=" O LEUB1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNB1 19 " --> pdb=" O ILEB1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 14 through 19' Processing helix chain 'B1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRB1 40 " --> pdb=" O METB1 36 " (cutoff:3.500A) Processing helix chain 'B1' and resid 42 through 58 Processing helix chain 'B1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSB1 74 " --> pdb=" O GLUB1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGB1 75 " --> pdb=" O ILEB1 71 " (cutoff:3.500A) Processing helix chain 'B1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSB1 81 " --> pdb=" O SERB1 77 " (cutoff:3.500A) Processing helix chain 'B1' and resid 168 through 176 Proline residue: B1 173 - end of helix Processing helix chain 'B1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUB1 188 " --> pdb=" O GLUB1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNB1 189 " --> pdb=" O LEUB1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEB1 191 " --> pdb=" O TYRB1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNB1 192 " --> pdb=" O GLUB1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERB1 202 " --> pdb=" O ARGB1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEB1 204 " --> pdb=" O SERB1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUB1 205 " --> pdb=" O GLYB1 201 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSB1 206 " --> pdb=" O SERB1 202 " (cutoff:3.500A) Processing helix chain 'B1' and resid 216 through 223 Processing helix chain 'B1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEB1 230 " --> pdb=" O GLUB1 226 " (cutoff:3.500A) Processing helix chain 'B1' and resid 263 through 280 Processing helix chain 'B1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUB1 286 " --> pdb=" O GLYB1 282 " (cutoff:3.500A) Processing helix chain 'B1' and resid 301 through 304 Processing helix chain 'B1' and resid 305 through 314 Processing helix chain 'B1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEB1 328 " --> pdb=" O LEUB1 324 " (cutoff:3.500A) Processing helix chain 'B1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSB1 352 " --> pdb=" O GLUB1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAB1 353 " --> pdb=" O TYRB1 349 " (cutoff:3.500A) Processing helix chain 'B1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSB1 372 " --> pdb=" O ALAB1 369 " (cutoff:3.500A) Processing helix chain 'C1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGC1 18 " --> pdb=" O LEUC1 14 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASNC1 19 " --> pdb=" O ILEC1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 14 through 19' Processing helix chain 'C1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRC1 40 " --> pdb=" O METC1 36 " (cutoff:3.500A) Processing helix chain 'C1' and resid 42 through 58 Processing helix chain 'C1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSC1 74 " --> pdb=" O GLUC1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGC1 75 " --> pdb=" O ILEC1 71 " (cutoff:3.500A) Processing helix chain 'C1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSC1 81 " --> pdb=" O SERC1 77 " (cutoff:3.500A) Processing helix chain 'C1' and resid 168 through 176 Proline residue: C1 173 - end of helix Processing helix chain 'C1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUC1 188 " --> pdb=" O GLUC1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNC1 189 " --> pdb=" O LEUC1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEC1 191 " --> pdb=" O TYRC1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNC1 192 " --> pdb=" O GLUC1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERC1 202 " --> pdb=" O ARGC1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEC1 204 " --> pdb=" O SERC1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUC1 205 " --> pdb=" O GLYC1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSC1 206 " --> pdb=" O SERC1 202 " (cutoff:3.500A) Processing helix chain 'C1' and resid 216 through 223 Processing helix chain 'C1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEC1 230 " --> pdb=" O GLUC1 226 " (cutoff:3.500A) Processing helix chain 'C1' and resid 263 through 280 Processing helix chain 'C1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUC1 286 " --> pdb=" O GLYC1 282 " (cutoff:3.500A) Processing helix chain 'C1' and resid 301 through 304 Processing helix chain 'C1' and resid 305 through 314 Processing helix chain 'C1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEC1 328 " --> pdb=" O LEUC1 324 " (cutoff:3.500A) Processing helix chain 'C1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSC1 352 " --> pdb=" O GLUC1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAC1 353 " --> pdb=" O TYRC1 349 " (cutoff:3.500A) Processing helix chain 'C1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSC1 372 " --> pdb=" O ALAC1 369 " (cutoff:3.500A) Processing helix chain 'D1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGD1 18 " --> pdb=" O LEUD1 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASND1 19 " --> pdb=" O ILED1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D1' and resid 14 through 19' Processing helix chain 'D1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRD1 40 " --> pdb=" O METD1 36 " (cutoff:3.500A) Processing helix chain 'D1' and resid 42 through 58 Processing helix chain 'D1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSD1 74 " --> pdb=" O GLUD1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGD1 75 " --> pdb=" O ILED1 71 " (cutoff:3.500A) Processing helix chain 'D1' and resid 76 through 91 removed outlier: 3.723A pdb=" N LYSD1 81 " --> pdb=" O SERD1 77 " (cutoff:3.500A) Processing helix chain 'D1' and resid 168 through 176 Proline residue: D1 173 - end of helix Processing helix chain 'D1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUD1 188 " --> pdb=" O GLUD1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLND1 189 " --> pdb=" O LEUD1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILED1 191 " --> pdb=" O TYRD1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASND1 192 " --> pdb=" O GLUD1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERD1 202 " --> pdb=" O ARGD1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILED1 204 " --> pdb=" O SERD1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUD1 205 " --> pdb=" O GLYD1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSD1 206 " --> pdb=" O SERD1 202 " (cutoff:3.500A) Processing helix chain 'D1' and resid 216 through 223 Processing helix chain 'D1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILED1 230 " --> pdb=" O GLUD1 226 " (cutoff:3.500A) Processing helix chain 'D1' and resid 263 through 280 Processing helix chain 'D1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUD1 286 " --> pdb=" O GLYD1 282 " (cutoff:3.500A) Processing helix chain 'D1' and resid 301 through 304 Processing helix chain 'D1' and resid 305 through 314 Processing helix chain 'D1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHED1 328 " --> pdb=" O LEUD1 324 " (cutoff:3.500A) Processing helix chain 'D1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSD1 352 " --> pdb=" O GLUD1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAD1 353 " --> pdb=" O TYRD1 349 " (cutoff:3.500A) Processing helix chain 'D1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSD1 372 " --> pdb=" O ALAD1 369 " (cutoff:3.500A) Processing helix chain 'E1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGE1 18 " --> pdb=" O LEUE1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNE1 19 " --> pdb=" O ILEE1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E1' and resid 14 through 19' Processing helix chain 'E1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRE1 40 " --> pdb=" O METE1 36 " (cutoff:3.500A) Processing helix chain 'E1' and resid 42 through 58 Processing helix chain 'E1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSE1 74 " --> pdb=" O GLUE1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGE1 75 " --> pdb=" O ILEE1 71 " (cutoff:3.500A) Processing helix chain 'E1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSE1 81 " --> pdb=" O SERE1 77 " (cutoff:3.500A) Processing helix chain 'E1' and resid 168 through 176 Proline residue: E1 173 - end of helix Processing helix chain 'E1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUE1 188 " --> pdb=" O GLUE1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNE1 189 " --> pdb=" O LEUE1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEE1 191 " --> pdb=" O TYRE1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNE1 192 " --> pdb=" O GLUE1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERE1 202 " --> pdb=" O ARGE1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEE1 204 " --> pdb=" O SERE1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUE1 205 " --> pdb=" O GLYE1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSE1 206 " --> pdb=" O SERE1 202 " (cutoff:3.500A) Processing helix chain 'E1' and resid 216 through 223 Processing helix chain 'E1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEE1 230 " --> pdb=" O GLUE1 226 " (cutoff:3.500A) Processing helix chain 'E1' and resid 263 through 280 Processing helix chain 'E1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUE1 286 " --> pdb=" O GLYE1 282 " (cutoff:3.500A) Processing helix chain 'E1' and resid 301 through 304 Processing helix chain 'E1' and resid 305 through 314 Processing helix chain 'E1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEE1 328 " --> pdb=" O LEUE1 324 " (cutoff:3.500A) Processing helix chain 'E1' and resid 347 through 359 removed outlier: 4.033A pdb=" N LYSE1 352 " --> pdb=" O GLUE1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAE1 353 " --> pdb=" O TYRE1 349 " (cutoff:3.500A) Processing helix chain 'E1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSE1 372 " --> pdb=" O ALAE1 369 " (cutoff:3.500A) Processing helix chain 'F1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGF1 18 " --> pdb=" O LEUF1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNF1 19 " --> pdb=" O ILEF1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'F1' and resid 14 through 19' Processing helix chain 'F1' and resid 32 through 42 removed outlier: 3.524A pdb=" N TYRF1 40 " --> pdb=" O METF1 36 " (cutoff:3.500A) Processing helix chain 'F1' and resid 42 through 58 Processing helix chain 'F1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSF1 74 " --> pdb=" O GLUF1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGF1 75 " --> pdb=" O ILEF1 71 " (cutoff:3.500A) Processing helix chain 'F1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSF1 81 " --> pdb=" O SERF1 77 " (cutoff:3.500A) Processing helix chain 'F1' and resid 168 through 176 Proline residue: F1 173 - end of helix Processing helix chain 'F1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUF1 188 " --> pdb=" O GLUF1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNF1 189 " --> pdb=" O LEUF1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEF1 191 " --> pdb=" O TYRF1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNF1 192 " --> pdb=" O GLUF1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERF1 202 " --> pdb=" O ARGF1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEF1 204 " --> pdb=" O SERF1 200 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLUF1 205 " --> pdb=" O GLYF1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSF1 206 " --> pdb=" O SERF1 202 " (cutoff:3.500A) Processing helix chain 'F1' and resid 216 through 223 Processing helix chain 'F1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEF1 230 " --> pdb=" O GLUF1 226 " (cutoff:3.500A) Processing helix chain 'F1' and resid 263 through 280 Processing helix chain 'F1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUF1 286 " --> pdb=" O GLYF1 282 " (cutoff:3.500A) Processing helix chain 'F1' and resid 301 through 304 Processing helix chain 'F1' and resid 305 through 314 Processing helix chain 'F1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEF1 328 " --> pdb=" O LEUF1 324 " (cutoff:3.500A) Processing helix chain 'F1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSF1 352 " --> pdb=" O GLUF1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAF1 353 " --> pdb=" O TYRF1 349 " (cutoff:3.500A) Processing helix chain 'F1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSF1 372 " --> pdb=" O ALAF1 369 " (cutoff:3.500A) Processing helix chain 'G1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGG1 18 " --> pdb=" O LEUG1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNG1 19 " --> pdb=" O ILEG1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G1' and resid 14 through 19' Processing helix chain 'G1' and resid 32 through 42 removed outlier: 3.526A pdb=" N TYRG1 40 " --> pdb=" O METG1 36 " (cutoff:3.500A) Processing helix chain 'G1' and resid 42 through 58 Processing helix chain 'G1' and resid 70 through 76 removed outlier: 3.618A pdb=" N LYSG1 74 " --> pdb=" O GLUG1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGG1 75 " --> pdb=" O ILEG1 71 " (cutoff:3.500A) Processing helix chain 'G1' and resid 76 through 91 removed outlier: 3.725A pdb=" N LYSG1 81 " --> pdb=" O SERG1 77 " (cutoff:3.500A) Processing helix chain 'G1' and resid 168 through 176 Proline residue: G1 173 - end of helix Processing helix chain 'G1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUG1 188 " --> pdb=" O GLUG1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNG1 189 " --> pdb=" O LEUG1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEG1 191 " --> pdb=" O TYRG1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNG1 192 " --> pdb=" O GLUG1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERG1 202 " --> pdb=" O ARGG1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEG1 204 " --> pdb=" O SERG1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUG1 205 " --> pdb=" O GLYG1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSG1 206 " --> pdb=" O SERG1 202 " (cutoff:3.500A) Processing helix chain 'G1' and resid 216 through 223 Processing helix chain 'G1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEG1 230 " --> pdb=" O GLUG1 226 " (cutoff:3.500A) Processing helix chain 'G1' and resid 263 through 280 Processing helix chain 'G1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUG1 286 " --> pdb=" O GLYG1 282 " (cutoff:3.500A) Processing helix chain 'G1' and resid 301 through 304 Processing helix chain 'G1' and resid 305 through 314 Processing helix chain 'G1' and resid 317 through 328 removed outlier: 3.527A pdb=" N PHEG1 328 " --> pdb=" O LEUG1 324 " (cutoff:3.500A) Processing helix chain 'G1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSG1 352 " --> pdb=" O GLUG1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAG1 353 " --> pdb=" O TYRG1 349 " (cutoff:3.500A) Processing helix chain 'G1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSG1 372 " --> pdb=" O ALAG1 369 " (cutoff:3.500A) Processing helix chain 'H1' and resid 14 through 19 removed outlier: 3.624A pdb=" N ARGH1 18 " --> pdb=" O LEUH1 14 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASNH1 19 " --> pdb=" O ILEH1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H1' and resid 14 through 19' Processing helix chain 'H1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRH1 40 " --> pdb=" O METH1 36 " (cutoff:3.500A) Processing helix chain 'H1' and resid 42 through 58 Processing helix chain 'H1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSH1 74 " --> pdb=" O GLUH1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGH1 75 " --> pdb=" O ILEH1 71 " (cutoff:3.500A) Processing helix chain 'H1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSH1 81 " --> pdb=" O SERH1 77 " (cutoff:3.500A) Processing helix chain 'H1' and resid 168 through 176 Proline residue: H1 173 - end of helix Processing helix chain 'H1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUH1 188 " --> pdb=" O GLUH1 184 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLNH1 189 " --> pdb=" O LEUH1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEH1 191 " --> pdb=" O TYRH1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNH1 192 " --> pdb=" O GLUH1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERH1 202 " --> pdb=" O ARGH1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEH1 204 " --> pdb=" O SERH1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUH1 205 " --> pdb=" O GLYH1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSH1 206 " --> pdb=" O SERH1 202 " (cutoff:3.500A) Processing helix chain 'H1' and resid 216 through 223 Processing helix chain 'H1' and resid 226 through 238 removed outlier: 3.527A pdb=" N ILEH1 230 " --> pdb=" O GLUH1 226 " (cutoff:3.500A) Processing helix chain 'H1' and resid 263 through 280 Processing helix chain 'H1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUH1 286 " --> pdb=" O GLYH1 282 " (cutoff:3.500A) Processing helix chain 'H1' and resid 301 through 304 Processing helix chain 'H1' and resid 305 through 314 Processing helix chain 'H1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEH1 328 " --> pdb=" O LEUH1 324 " (cutoff:3.500A) Processing helix chain 'H1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSH1 352 " --> pdb=" O GLUH1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAH1 353 " --> pdb=" O TYRH1 349 " (cutoff:3.500A) Processing helix chain 'H1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSH1 372 " --> pdb=" O ALAH1 369 " (cutoff:3.500A) Processing helix chain 'I1' and resid 14 through 19 removed outlier: 3.624A pdb=" N ARGI1 18 " --> pdb=" O LEUI1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNI1 19 " --> pdb=" O ILEI1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I1' and resid 14 through 19' Processing helix chain 'I1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRI1 40 " --> pdb=" O METI1 36 " (cutoff:3.500A) Processing helix chain 'I1' and resid 42 through 58 Processing helix chain 'I1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSI1 74 " --> pdb=" O GLUI1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGI1 75 " --> pdb=" O ILEI1 71 " (cutoff:3.500A) Processing helix chain 'I1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSI1 81 " --> pdb=" O SERI1 77 " (cutoff:3.500A) Processing helix chain 'I1' and resid 168 through 176 Proline residue: I1 173 - end of helix Processing helix chain 'I1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUI1 188 " --> pdb=" O GLUI1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNI1 189 " --> pdb=" O LEUI1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEI1 191 " --> pdb=" O TYRI1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNI1 192 " --> pdb=" O GLUI1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERI1 202 " --> pdb=" O ARGI1 198 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILEI1 204 " --> pdb=" O SERI1 200 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLUI1 205 " --> pdb=" O GLYI1 201 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYSI1 206 " --> pdb=" O SERI1 202 " (cutoff:3.500A) Processing helix chain 'I1' and resid 216 through 223 Processing helix chain 'I1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEI1 230 " --> pdb=" O GLUI1 226 " (cutoff:3.500A) Processing helix chain 'I1' and resid 263 through 280 Processing helix chain 'I1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUI1 286 " --> pdb=" O GLYI1 282 " (cutoff:3.500A) Processing helix chain 'I1' and resid 301 through 304 Processing helix chain 'I1' and resid 305 through 314 Processing helix chain 'I1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEI1 328 " --> pdb=" O LEUI1 324 " (cutoff:3.500A) Processing helix chain 'I1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSI1 352 " --> pdb=" O GLUI1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAI1 353 " --> pdb=" O TYRI1 349 " (cutoff:3.500A) Processing helix chain 'I1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSI1 372 " --> pdb=" O ALAI1 369 " (cutoff:3.500A) Processing helix chain 'J1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGJ1 18 " --> pdb=" O LEUJ1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNJ1 19 " --> pdb=" O ILEJ1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J1' and resid 14 through 19' Processing helix chain 'J1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRJ1 40 " --> pdb=" O METJ1 36 " (cutoff:3.500A) Processing helix chain 'J1' and resid 42 through 58 Processing helix chain 'J1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSJ1 74 " --> pdb=" O GLUJ1 70 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGJ1 75 " --> pdb=" O ILEJ1 71 " (cutoff:3.500A) Processing helix chain 'J1' and resid 76 through 91 removed outlier: 3.725A pdb=" N LYSJ1 81 " --> pdb=" O SERJ1 77 " (cutoff:3.500A) Processing helix chain 'J1' and resid 168 through 176 Proline residue: J1 173 - end of helix Processing helix chain 'J1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUJ1 188 " --> pdb=" O GLUJ1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNJ1 189 " --> pdb=" O LEUJ1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEJ1 191 " --> pdb=" O TYRJ1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNJ1 192 " --> pdb=" O GLUJ1 188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERJ1 202 " --> pdb=" O ARGJ1 198 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILEJ1 204 " --> pdb=" O SERJ1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUJ1 205 " --> pdb=" O GLYJ1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSJ1 206 " --> pdb=" O SERJ1 202 " (cutoff:3.500A) Processing helix chain 'J1' and resid 216 through 223 Processing helix chain 'J1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEJ1 230 " --> pdb=" O GLUJ1 226 " (cutoff:3.500A) Processing helix chain 'J1' and resid 263 through 280 Processing helix chain 'J1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUJ1 286 " --> pdb=" O GLYJ1 282 " (cutoff:3.500A) Processing helix chain 'J1' and resid 301 through 304 Processing helix chain 'J1' and resid 305 through 314 Processing helix chain 'J1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEJ1 328 " --> pdb=" O LEUJ1 324 " (cutoff:3.500A) Processing helix chain 'J1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSJ1 352 " --> pdb=" O GLUJ1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAJ1 353 " --> pdb=" O TYRJ1 349 " (cutoff:3.500A) Processing helix chain 'J1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSJ1 372 " --> pdb=" O ALAJ1 369 " (cutoff:3.500A) Processing helix chain 'K1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGK1 18 " --> pdb=" O LEUK1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNK1 19 " --> pdb=" O ILEK1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'K1' and resid 14 through 19' Processing helix chain 'K1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRK1 40 " --> pdb=" O METK1 36 " (cutoff:3.500A) Processing helix chain 'K1' and resid 42 through 58 Processing helix chain 'K1' and resid 70 through 76 removed outlier: 3.619A pdb=" N LYSK1 74 " --> pdb=" O GLUK1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGK1 75 " --> pdb=" O ILEK1 71 " (cutoff:3.500A) Processing helix chain 'K1' and resid 76 through 91 removed outlier: 3.723A pdb=" N LYSK1 81 " --> pdb=" O SERK1 77 " (cutoff:3.500A) Processing helix chain 'K1' and resid 168 through 176 Proline residue: K1 173 - end of helix Processing helix chain 'K1' and resid 181 through 206 removed outlier: 5.730A pdb=" N GLUK1 188 " --> pdb=" O GLUK1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNK1 189 " --> pdb=" O LEUK1 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEK1 191 " --> pdb=" O TYRK1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNK1 192 " --> pdb=" O GLUK1 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERK1 202 " --> pdb=" O ARGK1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEK1 204 " --> pdb=" O SERK1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUK1 205 " --> pdb=" O GLYK1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSK1 206 " --> pdb=" O SERK1 202 " (cutoff:3.500A) Processing helix chain 'K1' and resid 216 through 223 Processing helix chain 'K1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEK1 230 " --> pdb=" O GLUK1 226 " (cutoff:3.500A) Processing helix chain 'K1' and resid 263 through 280 Processing helix chain 'K1' and resid 282 through 288 removed outlier: 3.876A pdb=" N LEUK1 286 " --> pdb=" O GLYK1 282 " (cutoff:3.500A) Processing helix chain 'K1' and resid 301 through 304 Processing helix chain 'K1' and resid 305 through 314 Processing helix chain 'K1' and resid 317 through 328 removed outlier: 3.528A pdb=" N PHEK1 328 " --> pdb=" O LEUK1 324 " (cutoff:3.500A) Processing helix chain 'K1' and resid 347 through 359 removed outlier: 4.035A pdb=" N LYSK1 352 " --> pdb=" O GLUK1 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALAK1 353 " --> pdb=" O TYRK1 349 " (cutoff:3.500A) Processing helix chain 'K1' and resid 368 through 372 removed outlier: 3.747A pdb=" N LYSK1 372 " --> pdb=" O ALAK1 369 " (cutoff:3.500A) Processing helix chain 'L1' and resid 14 through 19 removed outlier: 3.625A pdb=" N ARGL1 18 " --> pdb=" O LEUL1 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASNL1 19 " --> pdb=" O ILEL1 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'L1' and resid 14 through 19' Processing helix chain 'L1' and resid 32 through 42 removed outlier: 3.525A pdb=" N TYRL1 40 " --> pdb=" O METL1 36 " (cutoff:3.500A) Processing helix chain 'L1' and resid 42 through 58 Processing helix chain 'L1' and resid 70 through 76 removed outlier: 3.620A pdb=" N LYSL1 74 " --> pdb=" O GLUL1 70 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGL1 75 " --> pdb=" O ILEL1 71 " (cutoff:3.500A) Processing helix chain 'L1' and resid 76 through 91 removed outlier: 3.724A pdb=" N LYSL1 81 " --> pdb=" O SERL1 77 " (cutoff:3.500A) Processing helix chain 'L1' and resid 168 through 176 Proline residue: L1 173 - end of helix Processing helix chain 'L1' and resid 181 through 206 removed outlier: 5.731A pdb=" N GLUL1 188 " --> pdb=" O GLUL1 184 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLNL1 189 " --> pdb=" O LEUL1 185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEL1 191 " --> pdb=" O TYRL1 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNL1 192 " --> pdb=" O GLUL1 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERL1 202 " --> pdb=" O ARGL1 198 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILEL1 204 " --> pdb=" O SERL1 200 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLUL1 205 " --> pdb=" O GLYL1 201 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSL1 206 " --> pdb=" O SERL1 202 " (cutoff:3.500A) Processing helix chain 'L1' and resid 216 through 223 Processing helix chain 'L1' and resid 226 through 238 removed outlier: 3.528A pdb=" N ILEL1 230 " --> pdb=" O GLUL1 226 " (cutoff:3.500A) Processing helix chain 'L1' and resid 263 through 280 Processing helix chain 'L1' and resid 282 through 288 removed outlier: 3.875A pdb=" N LEUL1 286 " --> pdb=" O GLYL1 282 " (cutoff:3.500A) Processing helix chain 'L1' and resid 301 through 304 Processing helix chain 'L1' and resid 305 through 314 Processing helix chain 'L1' and resid 317 through 328 removed outlier: 3.529A pdb=" N PHEL1 328 " --> pdb=" O LEUL1 324 " (cutoff:3.500A) Processing helix chain 'L1' and resid 347 through 359 removed outlier: 4.034A pdb=" N LYSL1 352 " --> pdb=" O GLUL1 348 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALAL1 353 " --> pdb=" O TYRL1 349 " (cutoff:3.500A) Processing helix chain 'L1' and resid 368 through 372 removed outlier: 3.746A pdb=" N LYSL1 372 " --> pdb=" O ALAL1 369 " (cutoff:3.500A) Processing helix chain 'A2' and resid 2 through 11 Processing helix chain 'A2' and resid 16 through 21 Processing helix chain 'A2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNA2 28 " --> pdb=" O PROA2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNA2 29 " --> pdb=" O VALA2 25 " (cutoff:3.500A) Processing helix chain 'A2' and resid 31 through 33 No H-bonds generated for 'chain 'A2' and resid 31 through 33' Processing helix chain 'A2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSA2 44 " --> pdb=" O ASNA2 40 " (cutoff:3.500A) Processing helix chain 'A2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERA2 62 " --> pdb=" O ASPA2 58 " (cutoff:3.500A) Processing helix chain 'A2' and resid 90 through 97 Processing helix chain 'A2' and resid 99 through 109 removed outlier: 3.829A pdb=" N META2 107 " --> pdb=" O GLNA2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRA2 109 " --> pdb=" O PHEA2 105 " (cutoff:3.500A) Processing helix chain 'B2' and resid 2 through 11 Processing helix chain 'B2' and resid 16 through 21 Processing helix chain 'B2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNB2 28 " --> pdb=" O PROB2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNB2 29 " --> pdb=" O VALB2 25 " (cutoff:3.500A) Processing helix chain 'B2' and resid 31 through 33 No H-bonds generated for 'chain 'B2' and resid 31 through 33' Processing helix chain 'B2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSB2 44 " --> pdb=" O ASNB2 40 " (cutoff:3.500A) Processing helix chain 'B2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERB2 62 " --> pdb=" O ASPB2 58 " (cutoff:3.500A) Processing helix chain 'B2' and resid 90 through 97 Processing helix chain 'B2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METB2 107 " --> pdb=" O GLNB2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRB2 109 " --> pdb=" O PHEB2 105 " (cutoff:3.500A) Processing helix chain 'C2' and resid 2 through 11 Processing helix chain 'C2' and resid 16 through 21 Processing helix chain 'C2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNC2 28 " --> pdb=" O PROC2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNC2 29 " --> pdb=" O VALC2 25 " (cutoff:3.500A) Processing helix chain 'C2' and resid 31 through 33 No H-bonds generated for 'chain 'C2' and resid 31 through 33' Processing helix chain 'C2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSC2 44 " --> pdb=" O ASNC2 40 " (cutoff:3.500A) Processing helix chain 'C2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERC2 62 " --> pdb=" O ASPC2 58 " (cutoff:3.500A) Processing helix chain 'C2' and resid 90 through 97 Processing helix chain 'C2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METC2 107 " --> pdb=" O GLNC2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRC2 109 " --> pdb=" O PHEC2 105 " (cutoff:3.500A) Processing helix chain 'D2' and resid 2 through 11 Processing helix chain 'D2' and resid 16 through 21 Processing helix chain 'D2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASND2 28 " --> pdb=" O PROD2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASND2 29 " --> pdb=" O VALD2 25 " (cutoff:3.500A) Processing helix chain 'D2' and resid 31 through 33 No H-bonds generated for 'chain 'D2' and resid 31 through 33' Processing helix chain 'D2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSD2 44 " --> pdb=" O ASND2 40 " (cutoff:3.500A) Processing helix chain 'D2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERD2 62 " --> pdb=" O ASPD2 58 " (cutoff:3.500A) Processing helix chain 'D2' and resid 90 through 97 Processing helix chain 'D2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METD2 107 " --> pdb=" O GLND2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRD2 109 " --> pdb=" O PHED2 105 " (cutoff:3.500A) Processing helix chain 'E2' and resid 2 through 11 Processing helix chain 'E2' and resid 16 through 21 Processing helix chain 'E2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNE2 28 " --> pdb=" O PROE2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNE2 29 " --> pdb=" O VALE2 25 " (cutoff:3.500A) Processing helix chain 'E2' and resid 31 through 33 No H-bonds generated for 'chain 'E2' and resid 31 through 33' Processing helix chain 'E2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSE2 44 " --> pdb=" O ASNE2 40 " (cutoff:3.500A) Processing helix chain 'E2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERE2 62 " --> pdb=" O ASPE2 58 " (cutoff:3.500A) Processing helix chain 'E2' and resid 90 through 97 Processing helix chain 'E2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METE2 107 " --> pdb=" O GLNE2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRE2 109 " --> pdb=" O PHEE2 105 " (cutoff:3.500A) Processing helix chain 'F2' and resid 2 through 11 Processing helix chain 'F2' and resid 16 through 21 Processing helix chain 'F2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNF2 28 " --> pdb=" O PROF2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNF2 29 " --> pdb=" O VALF2 25 " (cutoff:3.500A) Processing helix chain 'F2' and resid 31 through 33 No H-bonds generated for 'chain 'F2' and resid 31 through 33' Processing helix chain 'F2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSF2 44 " --> pdb=" O ASNF2 40 " (cutoff:3.500A) Processing helix chain 'F2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERF2 62 " --> pdb=" O ASPF2 58 " (cutoff:3.500A) Processing helix chain 'F2' and resid 90 through 97 Processing helix chain 'F2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METF2 107 " --> pdb=" O GLNF2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRF2 109 " --> pdb=" O PHEF2 105 " (cutoff:3.500A) Processing helix chain 'G2' and resid 2 through 11 Processing helix chain 'G2' and resid 16 through 21 Processing helix chain 'G2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNG2 28 " --> pdb=" O PROG2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNG2 29 " --> pdb=" O VALG2 25 " (cutoff:3.500A) Processing helix chain 'G2' and resid 31 through 33 No H-bonds generated for 'chain 'G2' and resid 31 through 33' Processing helix chain 'G2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSG2 44 " --> pdb=" O ASNG2 40 " (cutoff:3.500A) Processing helix chain 'G2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERG2 62 " --> pdb=" O ASPG2 58 " (cutoff:3.500A) Processing helix chain 'G2' and resid 90 through 97 Processing helix chain 'G2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METG2 107 " --> pdb=" O GLNG2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRG2 109 " --> pdb=" O PHEG2 105 " (cutoff:3.500A) Processing helix chain 'H2' and resid 2 through 11 Processing helix chain 'H2' and resid 16 through 21 Processing helix chain 'H2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNH2 28 " --> pdb=" O PROH2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNH2 29 " --> pdb=" O VALH2 25 " (cutoff:3.500A) Processing helix chain 'H2' and resid 31 through 33 No H-bonds generated for 'chain 'H2' and resid 31 through 33' Processing helix chain 'H2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSH2 44 " --> pdb=" O ASNH2 40 " (cutoff:3.500A) Processing helix chain 'H2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERH2 62 " --> pdb=" O ASPH2 58 " (cutoff:3.500A) Processing helix chain 'H2' and resid 90 through 97 Processing helix chain 'H2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METH2 107 " --> pdb=" O GLNH2 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THRH2 109 " --> pdb=" O PHEH2 105 " (cutoff:3.500A) Processing helix chain 'I2' and resid 2 through 11 Processing helix chain 'I2' and resid 16 through 21 Processing helix chain 'I2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNI2 28 " --> pdb=" O PROI2 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNI2 29 " --> pdb=" O VALI2 25 " (cutoff:3.500A) Processing helix chain 'I2' and resid 31 through 33 No H-bonds generated for 'chain 'I2' and resid 31 through 33' Processing helix chain 'I2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSI2 44 " --> pdb=" O ASNI2 40 " (cutoff:3.500A) Processing helix chain 'I2' and resid 58 through 63 removed outlier: 3.553A pdb=" N SERI2 62 " --> pdb=" O ASPI2 58 " (cutoff:3.500A) Processing helix chain 'I2' and resid 90 through 97 Processing helix chain 'I2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METI2 107 " --> pdb=" O GLNI2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRI2 109 " --> pdb=" O PHEI2 105 " (cutoff:3.500A) Processing helix chain 'J2' and resid 2 through 11 Processing helix chain 'J2' and resid 16 through 21 Processing helix chain 'J2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNJ2 28 " --> pdb=" O PROJ2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNJ2 29 " --> pdb=" O VALJ2 25 " (cutoff:3.500A) Processing helix chain 'J2' and resid 31 through 33 No H-bonds generated for 'chain 'J2' and resid 31 through 33' Processing helix chain 'J2' and resid 40 through 57 removed outlier: 3.619A pdb=" N LYSJ2 44 " --> pdb=" O ASNJ2 40 " (cutoff:3.500A) Processing helix chain 'J2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERJ2 62 " --> pdb=" O ASPJ2 58 " (cutoff:3.500A) Processing helix chain 'J2' and resid 90 through 97 Processing helix chain 'J2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METJ2 107 " --> pdb=" O GLNJ2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRJ2 109 " --> pdb=" O PHEJ2 105 " (cutoff:3.500A) Processing helix chain 'K2' and resid 2 through 11 Processing helix chain 'K2' and resid 16 through 21 Processing helix chain 'K2' and resid 22 through 30 removed outlier: 4.511A pdb=" N ASNK2 28 " --> pdb=" O PROK2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNK2 29 " --> pdb=" O VALK2 25 " (cutoff:3.500A) Processing helix chain 'K2' and resid 31 through 33 No H-bonds generated for 'chain 'K2' and resid 31 through 33' Processing helix chain 'K2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSK2 44 " --> pdb=" O ASNK2 40 " (cutoff:3.500A) Processing helix chain 'K2' and resid 58 through 63 removed outlier: 3.552A pdb=" N SERK2 62 " --> pdb=" O ASPK2 58 " (cutoff:3.500A) Processing helix chain 'K2' and resid 90 through 97 Processing helix chain 'K2' and resid 99 through 109 removed outlier: 3.828A pdb=" N METK2 107 " --> pdb=" O GLNK2 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THRK2 109 " --> pdb=" O PHEK2 105 " (cutoff:3.500A) Processing helix chain 'L2' and resid 2 through 11 Processing helix chain 'L2' and resid 16 through 21 Processing helix chain 'L2' and resid 22 through 30 removed outlier: 4.510A pdb=" N ASNL2 28 " --> pdb=" O PROL2 24 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASNL2 29 " --> pdb=" O VALL2 25 " (cutoff:3.500A) Processing helix chain 'L2' and resid 31 through 33 No H-bonds generated for 'chain 'L2' and resid 31 through 33' Processing helix chain 'L2' and resid 40 through 57 removed outlier: 3.620A pdb=" N LYSL2 44 " --> pdb=" O ASNL2 40 " (cutoff:3.500A) Processing helix chain 'L2' and resid 58 through 63 removed outlier: 3.553A pdb=" N SERL2 62 " --> pdb=" O ASPL2 58 " (cutoff:3.500A) Processing helix chain 'L2' and resid 90 through 97 Processing helix chain 'L2' and resid 99 through 109 removed outlier: 3.829A pdb=" N METL2 107 " --> pdb=" O GLNL2 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRL2 109 " --> pdb=" O PHEL2 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A1' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A1' and resid 117 through 122 removed outlier: 3.675A pdb=" N PHEA1 98 " --> pdb=" O LYSA1 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRA1 147 " --> pdb=" O ILEA1 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A1' and resid 253 through 258 removed outlier: 8.222A pdb=" N LEUL1 246 " --> pdb=" O SERA1 208 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHEA1 210 " --> pdb=" O LEUL1 246 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THRL1 248 " --> pdb=" O PHEA1 210 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYRA1 212 " --> pdb=" O THRL1 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A1' and resid 246 through 249 Processing sheet with id=AA6, first strand: chain 'B1' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'B1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEB1 98 " --> pdb=" O LYSB1 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B1' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'B1' and resid 246 through 248 Processing sheet with id=AB1, first strand: chain 'C1' and resid 61 through 63 Processing sheet with id=AB2, first strand: chain 'C1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEC1 98 " --> pdb=" O LYSC1 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRC1 147 " --> pdb=" O ILEC1 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C1' and resid 246 through 249 Processing sheet with id=AB5, first strand: chain 'D1' and resid 61 through 63 Processing sheet with id=AB6, first strand: chain 'D1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHED1 98 " --> pdb=" O LYSD1 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D1' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'D1' and resid 246 through 249 removed outlier: 6.787A pdb=" N LEUD1 246 " --> pdb=" O TYRE1 212 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILEE1 214 " --> pdb=" O LEUD1 246 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THRD1 248 " --> pdb=" O ILEE1 214 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E1' and resid 61 through 63 Processing sheet with id=AC1, first strand: chain 'E1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEE1 98 " --> pdb=" O LYSE1 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E1' and resid 146 through 147 Processing sheet with id=AC3, first strand: chain 'E1' and resid 246 through 249 Processing sheet with id=AC4, first strand: chain 'F1' and resid 61 through 63 Processing sheet with id=AC5, first strand: chain 'F1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEF1 98 " --> pdb=" O LYSF1 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRF1 147 " --> pdb=" O ILEF1 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F1' and resid 246 through 249 Processing sheet with id=AC8, first strand: chain 'G1' and resid 61 through 63 Processing sheet with id=AC9, first strand: chain 'G1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEG1 98 " --> pdb=" O LYSG1 118 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRG1 147 " --> pdb=" O ILEG1 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G1' and resid 246 through 249 Processing sheet with id=AD3, first strand: chain 'H1' and resid 61 through 63 Processing sheet with id=AD4, first strand: chain 'H1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEH1 98 " --> pdb=" O LYSH1 118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H1' and resid 146 through 147 removed outlier: 3.500A pdb=" N TYRH1 147 " --> pdb=" O ILEH1 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H1' and resid 246 through 249 Processing sheet with id=AD7, first strand: chain 'I1' and resid 61 through 63 Processing sheet with id=AD8, first strand: chain 'I1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEI1 98 " --> pdb=" O LYSI1 118 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I1' and resid 146 through 147 Processing sheet with id=AE1, first strand: chain 'I1' and resid 246 through 249 Processing sheet with id=AE2, first strand: chain 'J1' and resid 61 through 63 Processing sheet with id=AE3, first strand: chain 'J1' and resid 117 through 122 removed outlier: 3.674A pdb=" N PHEJ1 98 " --> pdb=" O LYSJ1 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J1' and resid 146 through 147 removed outlier: 3.501A pdb=" N TYRJ1 147 " --> pdb=" O ILEJ1 154 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J1' and resid 246 through 249 Processing sheet with id=AE6, first strand: chain 'K1' and resid 61 through 63 Processing sheet with id=AE7, first strand: chain 'K1' and resid 117 through 122 removed outlier: 3.673A pdb=" N PHEK1 98 " --> pdb=" O LYSK1 118 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K1' and resid 146 through 147 Processing sheet with id=AE9, first strand: chain 'K1' and resid 246 through 249 Processing sheet with id=AF1, first strand: chain 'L1' and resid 61 through 63 Processing sheet with id=AF2, first strand: chain 'L1' and resid 117 through 122 removed outlier: 3.673A pdb=" N PHEL1 98 " --> pdb=" O LYSL1 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L1' and resid 146 through 147 Processing sheet with id=AF4, first strand: chain 'A2' and resid 71 through 76 removed outlier: 6.228A pdb=" N ALAA2 72 " --> pdb=" O PHEA2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAL2 72 " --> pdb=" O PHEL2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAK2 72 " --> pdb=" O PHEK2 83 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALAJ2 72 " --> pdb=" O PHEJ2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAI2 72 " --> pdb=" O PHEI2 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALAH2 72 " --> pdb=" O PHEH2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAG2 72 " --> pdb=" O PHEG2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAF2 72 " --> pdb=" O PHEF2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAE2 72 " --> pdb=" O PHEE2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAD2 72 " --> pdb=" O PHED2 83 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALAC2 72 " --> pdb=" O PHEC2 83 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALAB2 72 " --> pdb=" O PHEB2 83 " (cutoff:3.500A) 1953 hydrogen bonds defined for protein. 5541 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.78 Time building geometry restraints manager: 18.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14968 1.34 - 1.46: 8303 1.46 - 1.57: 22761 1.57 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 46356 Sorted by residual: bond pdb=" CB GLND1 197 " pdb=" CG GLND1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.71e+00 bond pdb=" CB GLNA1 197 " pdb=" CG GLNA1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.67e+00 bond pdb=" CB GLNH1 197 " pdb=" CG GLNH1 197 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.64e+00 bond pdb=" CB GLNB1 197 " pdb=" CG GLNB1 197 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 bond pdb=" CB GLNK1 197 " pdb=" CG GLNK1 197 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.62e+00 ... (remaining 46351 not shown) Histogram of bond angle deviations from ideal: 92.57 - 100.85: 85 100.85 - 109.14: 2809 109.14 - 117.42: 30142 117.42 - 125.70: 29076 125.70 - 133.99: 408 Bond angle restraints: 62520 Sorted by residual: angle pdb=" CG META2 107 " pdb=" SD META2 107 " pdb=" CE META2 107 " ideal model delta sigma weight residual 100.90 92.57 8.33 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METF2 107 " pdb=" SD METF2 107 " pdb=" CE METF2 107 " ideal model delta sigma weight residual 100.90 92.57 8.33 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METH2 107 " pdb=" SD METH2 107 " pdb=" CE METH2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METI2 107 " pdb=" SD METI2 107 " pdb=" CE METI2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CG METD2 107 " pdb=" SD METD2 107 " pdb=" CE METD2 107 " ideal model delta sigma weight residual 100.90 92.58 8.32 2.20e+00 2.07e-01 1.43e+01 ... (remaining 62515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 24229 16.37 - 32.74: 2805 32.74 - 49.10: 758 49.10 - 65.47: 120 65.47 - 81.84: 48 Dihedral angle restraints: 27960 sinusoidal: 11280 harmonic: 16680 Sorted by residual: dihedral pdb=" CA LEUF2 106 " pdb=" C LEUF2 106 " pdb=" N METF2 107 " pdb=" CA METF2 107 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LEUB2 106 " pdb=" C LEUB2 106 " pdb=" N METB2 107 " pdb=" CA METB2 107 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEUC2 106 " pdb=" C LEUC2 106 " pdb=" N METC2 107 " pdb=" CA METC2 107 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 27957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3578 0.029 - 0.059: 1988 0.059 - 0.088: 913 0.088 - 0.118: 357 0.118 - 0.147: 40 Chirality restraints: 6876 Sorted by residual: chirality pdb=" CA CYSB2 32 " pdb=" N CYSB2 32 " pdb=" C CYSB2 32 " pdb=" CB CYSB2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA CYSJ2 32 " pdb=" N CYSJ2 32 " pdb=" C CYSJ2 32 " pdb=" CB CYSJ2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA CYSI2 32 " pdb=" N CYSI2 32 " pdb=" C CYSI2 32 " pdb=" CB CYSI2 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 6873 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALE2 23 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PROE2 24 " 0.098 5.00e-02 4.00e+02 pdb=" CA PROE2 24 " -0.029 5.00e-02 4.00e+02 pdb=" CD PROE2 24 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALK2 23 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PROK2 24 " -0.098 5.00e-02 4.00e+02 pdb=" CA PROK2 24 " 0.029 5.00e-02 4.00e+02 pdb=" CD PROK2 24 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALF2 23 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PROF2 24 " 0.097 5.00e-02 4.00e+02 pdb=" CA PROF2 24 " -0.029 5.00e-02 4.00e+02 pdb=" CD PROF2 24 " -0.032 5.00e-02 4.00e+02 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 463 2.46 - 3.07: 35429 3.07 - 3.68: 71360 3.68 - 4.29: 106267 4.29 - 4.90: 166190 Nonbonded interactions: 379709 Sorted by model distance: nonbonded pdb=" NE2 GLNH1 197 " pdb=" OE1 GLNI1 189 " model vdw 1.854 2.520 nonbonded pdb=" OH TYRK1 55 " pdb=" OD2 ASPL1 307 " model vdw 1.906 2.440 nonbonded pdb=" NE2 GLNK1 197 " pdb=" OE1 GLNL1 189 " model vdw 1.910 2.520 nonbonded pdb=" O ARGK1 25 " pdb=" N ASPL1 9 " model vdw 1.966 2.520 nonbonded pdb=" NE2 GLND1 197 " pdb=" OE1 GLNE1 189 " model vdw 1.973 2.520 ... (remaining 379704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A1' selection = chain 'B1' selection = chain 'C1' selection = chain 'D1' selection = chain 'E1' selection = chain 'F1' selection = chain 'G1' selection = chain 'H1' selection = chain 'I1' selection = chain 'J1' selection = chain 'K1' selection = chain 'L1' } ncs_group { reference = chain 'A2' selection = chain 'B2' selection = chain 'C2' selection = chain 'D2' selection = chain 'E2' selection = chain 'F2' selection = chain 'G2' selection = chain 'H2' selection = chain 'I2' selection = chain 'J2' selection = chain 'K2' selection = chain 'L2' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 29.020 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 114.170 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 46356 Z= 0.463 Angle : 0.860 8.334 62520 Z= 0.473 Chirality : 0.045 0.147 6876 Planarity : 0.004 0.057 8064 Dihedral : 15.041 81.840 17292 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 0.48 % Allowed : 0.42 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.11), residues: 5676 helix: -0.46 (0.11), residues: 2292 sheet: 1.38 (0.29), residues: 288 loop : -1.79 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPF2 95 HIS 0.004 0.001 HISJ1 155 PHE 0.014 0.002 PHEG2 117 TYR 0.032 0.003 TYRL1 177 ARG 0.016 0.001 ARGE1 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1543 time to evaluate : 5.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B1 21 MET cc_start: 0.8240 (mmm) cc_final: 0.7927 (mmp) REVERT: B1 73 LYS cc_start: 0.7534 (tptt) cc_final: 0.7286 (ttmm) REVERT: B1 82 ASN cc_start: 0.8757 (m110) cc_final: 0.8479 (m110) REVERT: B1 227 GLU cc_start: 0.7893 (tp30) cc_final: 0.7468 (tp30) REVERT: B1 236 CYS cc_start: 0.8438 (t) cc_final: 0.8218 (t) REVERT: C1 33 ASP cc_start: 0.7726 (t70) cc_final: 0.7332 (t70) REVERT: C1 82 ASN cc_start: 0.8507 (m110) cc_final: 0.8279 (m110) REVERT: C1 156 TRP cc_start: 0.7028 (t60) cc_final: 0.6795 (t-100) REVERT: C1 236 CYS cc_start: 0.8416 (t) cc_final: 0.8196 (t) REVERT: C1 326 GLU cc_start: 0.8233 (pp20) cc_final: 0.8000 (pp20) REVERT: D1 82 ASN cc_start: 0.8285 (m110) cc_final: 0.8024 (m110) REVERT: D1 176 TYR cc_start: 0.5423 (m-80) cc_final: 0.5206 (m-80) REVERT: D1 227 GLU cc_start: 0.7864 (tp30) cc_final: 0.7457 (tp30) REVERT: D1 236 CYS cc_start: 0.8387 (t) cc_final: 0.8112 (t) REVERT: E1 84 THR cc_start: 0.9116 (t) cc_final: 0.8657 (p) REVERT: E1 166 MET cc_start: 0.7523 (mtm) cc_final: 0.7176 (mtt) REVERT: E1 200 SER cc_start: 0.9151 (p) cc_final: 0.8922 (p) REVERT: E1 268 ASP cc_start: 0.8033 (t0) cc_final: 0.7747 (t0) REVERT: E1 326 GLU cc_start: 0.8269 (pp20) cc_final: 0.7961 (pp20) REVERT: F1 84 THR cc_start: 0.9142 (t) cc_final: 0.8612 (p) REVERT: F1 175 TYR cc_start: 0.8243 (m-80) cc_final: 0.7956 (m-80) REVERT: F1 200 SER cc_start: 0.9212 (p) cc_final: 0.8948 (p) REVERT: F1 373 ASP cc_start: 0.6811 (t0) cc_final: 0.6576 (t0) REVERT: G1 200 SER cc_start: 0.9240 (p) cc_final: 0.9037 (p) REVERT: G1 301 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7486 (mp0) REVERT: G1 373 ASP cc_start: 0.7008 (t0) cc_final: 0.6774 (t0) REVERT: H1 98 PHE cc_start: 0.8582 (p90) cc_final: 0.8349 (p90) REVERT: H1 103 ASP cc_start: 0.7648 (m-30) cc_final: 0.7367 (m-30) REVERT: H1 214 ILE cc_start: 0.8496 (mt) cc_final: 0.8237 (mt) REVERT: H1 269 ASN cc_start: 0.8606 (t0) cc_final: 0.8398 (t0) REVERT: H1 273 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7612 (tpp80) REVERT: H1 301 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7300 (mp0) REVERT: H1 316 TYR cc_start: 0.8902 (m-80) cc_final: 0.8698 (m-10) REVERT: H1 373 ASP cc_start: 0.7189 (t0) cc_final: 0.6877 (t0) REVERT: I1 33 ASP cc_start: 0.7474 (t70) cc_final: 0.7125 (t70) REVERT: I1 103 ASP cc_start: 0.7730 (m-30) cc_final: 0.7520 (m-30) REVERT: I1 175 TYR cc_start: 0.8180 (m-80) cc_final: 0.7906 (m-80) REVERT: I1 200 SER cc_start: 0.9164 (p) cc_final: 0.8917 (p) REVERT: I1 214 ILE cc_start: 0.8332 (mt) cc_final: 0.8109 (mt) REVERT: I1 249 ASP cc_start: 0.6876 (m-30) cc_final: 0.6668 (m-30) REVERT: I1 326 GLU cc_start: 0.8136 (pp20) cc_final: 0.7822 (pp20) REVERT: J1 103 ASP cc_start: 0.7489 (m-30) cc_final: 0.7280 (m-30) REVERT: J1 166 MET cc_start: 0.7515 (mtm) cc_final: 0.7156 (mtt) REVERT: J1 175 TYR cc_start: 0.8126 (m-80) cc_final: 0.7670 (m-80) REVERT: J1 176 TYR cc_start: 0.5446 (m-80) cc_final: 0.5216 (m-80) REVERT: J1 180 MET cc_start: 0.8371 (ttm) cc_final: 0.8094 (ttt) REVERT: J1 273 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7818 (tpp80) REVERT: J1 301 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7170 (mp0) REVERT: J1 334 GLU cc_start: 0.6692 (mp0) cc_final: 0.6453 (mp0) REVERT: K1 236 CYS cc_start: 0.8496 (t) cc_final: 0.8222 (t) REVERT: K1 273 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7560 (tpp80) REVERT: L1 190 PHE cc_start: 0.8459 (t80) cc_final: 0.8214 (t80) REVERT: L1 318 GLU cc_start: 0.8295 (tt0) cc_final: 0.8055 (mt-10) REVERT: A2 43 ASP cc_start: 0.7501 (t0) cc_final: 0.7151 (t0) REVERT: A2 90 SER cc_start: 0.8949 (t) cc_final: 0.8719 (t) REVERT: B2 34 TYR cc_start: 0.8480 (t80) cc_final: 0.8269 (t80) REVERT: B2 43 ASP cc_start: 0.7415 (t0) cc_final: 0.7053 (t0) REVERT: B2 90 SER cc_start: 0.8981 (t) cc_final: 0.8744 (t) REVERT: B2 113 MET cc_start: 0.8197 (ttp) cc_final: 0.7905 (ttp) REVERT: C2 43 ASP cc_start: 0.7964 (t0) cc_final: 0.7708 (t0) REVERT: C2 90 SER cc_start: 0.8948 (t) cc_final: 0.8657 (t) REVERT: D2 90 SER cc_start: 0.8909 (t) cc_final: 0.8696 (t) REVERT: E2 11 PHE cc_start: 0.8608 (m-80) cc_final: 0.8406 (m-10) REVERT: E2 43 ASP cc_start: 0.7574 (t0) cc_final: 0.7229 (t0) REVERT: E2 90 SER cc_start: 0.8961 (t) cc_final: 0.8734 (t) REVERT: E2 113 MET cc_start: 0.8236 (ttp) cc_final: 0.8007 (ttp) REVERT: F2 11 PHE cc_start: 0.8695 (m-80) cc_final: 0.8368 (m-10) REVERT: F2 90 SER cc_start: 0.8960 (t) cc_final: 0.8692 (t) REVERT: G2 43 ASP cc_start: 0.7819 (t0) cc_final: 0.7441 (t0) REVERT: G2 90 SER cc_start: 0.8985 (t) cc_final: 0.8758 (t) REVERT: H2 11 PHE cc_start: 0.8643 (m-80) cc_final: 0.8344 (m-10) REVERT: H2 90 SER cc_start: 0.8923 (t) cc_final: 0.8690 (t) REVERT: I2 43 ASP cc_start: 0.7609 (t0) cc_final: 0.7317 (t0) REVERT: I2 90 SER cc_start: 0.8797 (t) cc_final: 0.8469 (t) REVERT: J2 90 SER cc_start: 0.8947 (t) cc_final: 0.8721 (t) REVERT: K2 90 SER cc_start: 0.9047 (t) cc_final: 0.8810 (t) REVERT: L2 15 ASP cc_start: 0.7822 (m-30) cc_final: 0.7575 (m-30) REVERT: L2 43 ASP cc_start: 0.7745 (t0) cc_final: 0.7544 (t0) REVERT: L2 90 SER cc_start: 0.8914 (t) cc_final: 0.8682 (t) outliers start: 24 outliers final: 1 residues processed: 1551 average time/residue: 0.5281 time to fit residues: 1388.9779 Evaluate side-chains 1349 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1348 time to evaluate : 5.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I1 residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 476 optimal weight: 0.3980 chunk 427 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 288 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 442 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 268 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 512 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 82 ASN ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 313 GLN ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 313 GLN ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 313 GLN ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 313 GLN E1 222 GLN ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 313 GLN F1 82 ASN F1 222 GLN ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 313 GLN G1 222 GLN ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 313 GLN H1 222 GLN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 313 GLN I1 82 ASN ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 313 GLN J1 82 ASN ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 313 GLN K1 82 ASN ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 313 GLN L1 82 ASN ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 313 GLN ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46356 Z= 0.249 Angle : 0.711 9.841 62520 Z= 0.375 Chirality : 0.044 0.161 6876 Planarity : 0.004 0.054 8064 Dihedral : 5.913 24.534 6338 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 1.60 % Allowed : 14.19 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.11), residues: 5676 helix: -0.35 (0.10), residues: 2544 sheet: 1.02 (0.30), residues: 288 loop : -1.75 (0.12), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPH2 95 HIS 0.003 0.001 HISB1 155 PHE 0.018 0.002 PHEG1 122 TYR 0.023 0.003 TYRF1 141 ARG 0.013 0.001 ARGF1 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1480 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 326 GLU cc_start: 0.7927 (pp20) cc_final: 0.7641 (pp20) REVERT: A1 373 ASP cc_start: 0.6588 (t0) cc_final: 0.6298 (t0) REVERT: B1 33 ASP cc_start: 0.7347 (t70) cc_final: 0.7027 (t70) REVERT: B1 274 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7358 (tpp80) REVERT: C1 33 ASP cc_start: 0.7290 (t70) cc_final: 0.6996 (t70) REVERT: C1 73 LYS cc_start: 0.7770 (tptt) cc_final: 0.7459 (ttmm) REVERT: C1 301 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7301 (mp0) REVERT: D1 82 ASN cc_start: 0.8270 (m110) cc_final: 0.8052 (m110) REVERT: D1 122 PHE cc_start: 0.8621 (m-80) cc_final: 0.8227 (m-80) REVERT: D1 197 GLN cc_start: 0.8545 (tt0) cc_final: 0.8306 (tt0) REVERT: D1 277 MET cc_start: 0.8452 (tpt) cc_final: 0.8227 (tpt) REVERT: D1 301 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7274 (mp0) REVERT: E1 162 PHE cc_start: 0.8279 (m-80) cc_final: 0.8078 (m-80) REVERT: E1 166 MET cc_start: 0.7678 (mtm) cc_final: 0.7323 (mtt) REVERT: E1 273 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7377 (tpp80) REVERT: E1 373 ASP cc_start: 0.6838 (t0) cc_final: 0.6600 (t0) REVERT: F1 316 TYR cc_start: 0.8761 (m-10) cc_final: 0.8133 (m-10) REVERT: F1 322 ASN cc_start: 0.8606 (t0) cc_final: 0.8373 (t0) REVERT: F1 373 ASP cc_start: 0.6869 (t0) cc_final: 0.6644 (t0) REVERT: G1 277 MET cc_start: 0.8451 (tpt) cc_final: 0.8007 (tpt) REVERT: G1 301 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7298 (mp0) REVERT: G1 334 GLU cc_start: 0.6498 (mp0) cc_final: 0.6126 (mp0) REVERT: H1 73 LYS cc_start: 0.7747 (tptt) cc_final: 0.7204 (ttmm) REVERT: H1 171 GLU cc_start: 0.8145 (pt0) cc_final: 0.7574 (pt0) REVERT: H1 301 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7237 (mp0) REVERT: H1 326 GLU cc_start: 0.7960 (pp20) cc_final: 0.7723 (pp20) REVERT: H1 373 ASP cc_start: 0.7256 (t0) cc_final: 0.6931 (t0) REVERT: I1 175 TYR cc_start: 0.7935 (m-80) cc_final: 0.7670 (m-80) REVERT: J1 175 TYR cc_start: 0.7842 (m-80) cc_final: 0.7335 (m-80) REVERT: J1 187 TYR cc_start: 0.8499 (t80) cc_final: 0.8278 (t80) REVERT: J1 273 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7876 (mmt90) REVERT: J1 277 MET cc_start: 0.8383 (tpt) cc_final: 0.8144 (tpt) REVERT: J1 301 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7150 (mp0) REVERT: J1 326 GLU cc_start: 0.8169 (pp20) cc_final: 0.7914 (pp20) REVERT: J1 327 ILE cc_start: 0.8603 (tt) cc_final: 0.8173 (tt) REVERT: K1 73 LYS cc_start: 0.7818 (tptt) cc_final: 0.7333 (ttmm) REVERT: K1 273 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7018 (ttm-80) REVERT: K1 277 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8102 (tpt) REVERT: L1 73 LYS cc_start: 0.7534 (tttp) cc_final: 0.7289 (ttmm) REVERT: L1 92 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7818 (tpp80) REVERT: L1 190 PHE cc_start: 0.8584 (t80) cc_final: 0.8278 (t80) REVERT: L1 326 GLU cc_start: 0.7925 (pp20) cc_final: 0.7541 (pp20) REVERT: A2 15 ASP cc_start: 0.7871 (m-30) cc_final: 0.7547 (m-30) REVERT: A2 49 LEU cc_start: 0.9205 (mt) cc_final: 0.9001 (mt) REVERT: A2 90 SER cc_start: 0.8757 (t) cc_final: 0.8448 (t) REVERT: B2 15 ASP cc_start: 0.7696 (m-30) cc_final: 0.7429 (m-30) REVERT: B2 43 ASP cc_start: 0.7515 (t0) cc_final: 0.6579 (t70) REVERT: B2 90 SER cc_start: 0.8745 (t) cc_final: 0.8466 (t) REVERT: C2 43 ASP cc_start: 0.7569 (t0) cc_final: 0.7153 (t70) REVERT: C2 90 SER cc_start: 0.8725 (t) cc_final: 0.8444 (t) REVERT: D2 15 ASP cc_start: 0.7770 (m-30) cc_final: 0.7414 (m-30) REVERT: D2 90 SER cc_start: 0.8723 (t) cc_final: 0.8461 (t) REVERT: E2 15 ASP cc_start: 0.7756 (m-30) cc_final: 0.7414 (m-30) REVERT: E2 90 SER cc_start: 0.8736 (t) cc_final: 0.8454 (t) REVERT: F2 1 MET cc_start: 0.6522 (mmt) cc_final: 0.5169 (mmt) REVERT: F2 43 ASP cc_start: 0.7427 (t0) cc_final: 0.6890 (t0) REVERT: F2 90 SER cc_start: 0.8757 (t) cc_final: 0.8520 (t) REVERT: G2 43 ASP cc_start: 0.7560 (t0) cc_final: 0.6981 (t0) REVERT: G2 47 ILE cc_start: 0.8920 (mm) cc_final: 0.8705 (mm) REVERT: G2 90 SER cc_start: 0.8879 (t) cc_final: 0.8633 (t) REVERT: H2 90 SER cc_start: 0.8688 (t) cc_final: 0.8438 (t) REVERT: I2 90 SER cc_start: 0.8654 (t) cc_final: 0.8290 (t) REVERT: J2 90 SER cc_start: 0.8845 (t) cc_final: 0.8586 (t) REVERT: K2 90 SER cc_start: 0.8765 (t) cc_final: 0.8538 (t) REVERT: L2 15 ASP cc_start: 0.7782 (m-30) cc_final: 0.7445 (m-30) REVERT: L2 90 SER cc_start: 0.8817 (t) cc_final: 0.8561 (t) outliers start: 80 outliers final: 49 residues processed: 1510 average time/residue: 0.5350 time to fit residues: 1364.2901 Evaluate side-chains 1362 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1312 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 131 ASN Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 246 LEU Chi-restraints excluded: chain D1 residue 246 LEU Chi-restraints excluded: chain E1 residue 74 LYS Chi-restraints excluded: chain E1 residue 246 LEU Chi-restraints excluded: chain E1 residue 371 LEU Chi-restraints excluded: chain F1 residue 371 LEU Chi-restraints excluded: chain G1 residue 74 LYS Chi-restraints excluded: chain G1 residue 371 LEU Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 74 LYS Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 131 ASN Chi-restraints excluded: chain H1 residue 309 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 74 LYS Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 74 LYS Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 277 MET Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 131 ASN Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 82 SER Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain F2 residue 113 MET Chi-restraints excluded: chain G2 residue 13 ASN Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 82 SER Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 426 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 513 optimal weight: 0.9990 chunk 554 optimal weight: 0.9980 chunk 456 optimal weight: 0.9990 chunk 508 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 82 ASN ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 82 ASN ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 82 ASN ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 82 ASN ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 311 ASN ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46356 Z= 0.270 Angle : 0.693 9.653 62520 Z= 0.358 Chirality : 0.043 0.155 6876 Planarity : 0.004 0.052 8064 Dihedral : 5.613 21.354 6336 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.72 % Allowed : 19.12 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.11), residues: 5676 helix: -0.15 (0.10), residues: 2472 sheet: 1.00 (0.29), residues: 288 loop : -1.69 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPC2 95 HIS 0.003 0.001 HISB1 155 PHE 0.020 0.002 PHEE2 117 TYR 0.025 0.002 TYRH1 177 ARG 0.009 0.000 ARGA1 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1407 time to evaluate : 5.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 326 GLU cc_start: 0.7939 (pp20) cc_final: 0.7710 (pp20) REVERT: A1 350 ASP cc_start: 0.8540 (t0) cc_final: 0.8293 (t0) REVERT: B1 33 ASP cc_start: 0.7212 (t70) cc_final: 0.6859 (t0) REVERT: B1 274 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7504 (tpp80) REVERT: C1 82 ASN cc_start: 0.8407 (m-40) cc_final: 0.8134 (m110) REVERT: C1 87 MET cc_start: 0.8550 (tpp) cc_final: 0.8252 (tpp) REVERT: C1 180 MET cc_start: 0.7979 (tpp) cc_final: 0.7502 (tpp) REVERT: C1 301 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7288 (mp0) REVERT: C1 326 GLU cc_start: 0.8175 (pp20) cc_final: 0.7932 (pp20) REVERT: D1 36 MET cc_start: 0.7794 (mtm) cc_final: 0.7500 (ttm) REVERT: D1 87 MET cc_start: 0.8472 (tpp) cc_final: 0.8245 (tpp) REVERT: D1 122 PHE cc_start: 0.8737 (m-80) cc_final: 0.8461 (m-80) REVERT: D1 197 GLN cc_start: 0.8473 (tt0) cc_final: 0.8172 (tt0) REVERT: D1 274 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7502 (tpp80) REVERT: D1 277 MET cc_start: 0.8456 (tpt) cc_final: 0.8076 (tpt) REVERT: D1 301 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7273 (mp0) REVERT: E1 45 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: E1 103 ASP cc_start: 0.7688 (m-30) cc_final: 0.7342 (m-30) REVERT: E1 143 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7376 (mmmt) REVERT: E1 217 TYR cc_start: 0.8179 (t80) cc_final: 0.7941 (t80) REVERT: E1 273 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7612 (mmm-85) REVERT: E1 274 ARG cc_start: 0.8541 (tpp80) cc_final: 0.7814 (tpp80) REVERT: E1 316 TYR cc_start: 0.8523 (m-10) cc_final: 0.8117 (m-10) REVERT: F1 103 ASP cc_start: 0.7510 (m-30) cc_final: 0.7295 (m-30) REVERT: F1 274 ARG cc_start: 0.8536 (tpp80) cc_final: 0.7595 (tpp80) REVERT: F1 316 TYR cc_start: 0.8741 (m-80) cc_final: 0.8161 (m-10) REVERT: F1 322 ASN cc_start: 0.8660 (t0) cc_final: 0.8396 (t0) REVERT: F1 326 GLU cc_start: 0.8418 (pp20) cc_final: 0.7852 (pp20) REVERT: F1 327 ILE cc_start: 0.8471 (tt) cc_final: 0.8270 (tt) REVERT: F1 373 ASP cc_start: 0.6951 (t0) cc_final: 0.6741 (t0) REVERT: G1 21 MET cc_start: 0.8591 (mmt) cc_final: 0.8249 (mmt) REVERT: G1 82 ASN cc_start: 0.7578 (m-40) cc_final: 0.7282 (m110) REVERT: G1 277 MET cc_start: 0.8361 (tpt) cc_final: 0.7912 (tpt) REVERT: G1 301 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7244 (mp0) REVERT: H1 73 LYS cc_start: 0.7738 (tptt) cc_final: 0.7224 (ttmm) REVERT: H1 182 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7447 (mp0) REVERT: H1 273 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7462 (mmm-85) REVERT: H1 301 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7296 (mp0) REVERT: H1 316 TYR cc_start: 0.8859 (m-10) cc_final: 0.8643 (m-10) REVERT: H1 326 GLU cc_start: 0.8028 (pp20) cc_final: 0.7808 (pp20) REVERT: H1 330 LEU cc_start: 0.8592 (mm) cc_final: 0.8365 (mm) REVERT: H1 373 ASP cc_start: 0.7324 (t0) cc_final: 0.7087 (t0) REVERT: I1 175 TYR cc_start: 0.8080 (m-80) cc_final: 0.7779 (m-80) REVERT: I1 272 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8503 (mm) REVERT: I1 350 ASP cc_start: 0.8873 (t0) cc_final: 0.8632 (t0) REVERT: J1 39 MET cc_start: 0.9223 (mtt) cc_final: 0.8997 (mtt) REVERT: J1 87 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8105 (tpp) REVERT: J1 171 GLU cc_start: 0.8322 (pt0) cc_final: 0.8012 (pt0) REVERT: J1 274 ARG cc_start: 0.8549 (tpp80) cc_final: 0.7475 (tpp80) REVERT: J1 301 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7033 (mp0) REVERT: J1 327 ILE cc_start: 0.8612 (tt) cc_final: 0.8134 (tt) REVERT: J1 350 ASP cc_start: 0.8909 (t0) cc_final: 0.8664 (t0) REVERT: K1 45 MET cc_start: 0.7965 (ttm) cc_final: 0.7742 (mtm) REVERT: K1 274 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7368 (tpp80) REVERT: K1 277 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8034 (tpt) REVERT: L1 73 LYS cc_start: 0.7654 (tttp) cc_final: 0.7444 (ttmm) REVERT: L1 326 GLU cc_start: 0.7855 (pp20) cc_final: 0.7590 (pp20) REVERT: A2 15 ASP cc_start: 0.7959 (m-30) cc_final: 0.7528 (m-30) REVERT: A2 90 SER cc_start: 0.8824 (t) cc_final: 0.8559 (t) REVERT: B2 15 ASP cc_start: 0.7779 (m-30) cc_final: 0.7298 (m-30) REVERT: B2 43 ASP cc_start: 0.7398 (t0) cc_final: 0.6694 (t70) REVERT: B2 90 SER cc_start: 0.8856 (t) cc_final: 0.8551 (t) REVERT: C2 15 ASP cc_start: 0.8056 (m-30) cc_final: 0.7604 (m-30) REVERT: C2 43 ASP cc_start: 0.7662 (t0) cc_final: 0.7343 (t70) REVERT: C2 90 SER cc_start: 0.8823 (t) cc_final: 0.8561 (t) REVERT: C2 107 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7700 (mtp) REVERT: D2 15 ASP cc_start: 0.7856 (m-30) cc_final: 0.7386 (m-30) REVERT: D2 90 SER cc_start: 0.8828 (t) cc_final: 0.8546 (t) REVERT: D2 107 MET cc_start: 0.8321 (mtm) cc_final: 0.8103 (mtp) REVERT: E2 15 ASP cc_start: 0.7816 (m-30) cc_final: 0.7380 (m-30) REVERT: E2 90 SER cc_start: 0.8773 (t) cc_final: 0.8489 (t) REVERT: F2 1 MET cc_start: 0.6422 (mmt) cc_final: 0.5078 (mmt) REVERT: F2 90 SER cc_start: 0.8841 (t) cc_final: 0.8578 (t) REVERT: F2 107 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: G2 90 SER cc_start: 0.8956 (t) cc_final: 0.8680 (t) REVERT: H2 5 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7802 (t70) REVERT: H2 15 ASP cc_start: 0.7843 (m-30) cc_final: 0.7634 (m-30) REVERT: H2 90 SER cc_start: 0.8752 (t) cc_final: 0.8370 (t) REVERT: I2 90 SER cc_start: 0.8827 (t) cc_final: 0.8504 (t) REVERT: J2 15 ASP cc_start: 0.7788 (m-30) cc_final: 0.7569 (m-30) REVERT: J2 90 SER cc_start: 0.8910 (t) cc_final: 0.8645 (t) REVERT: K2 41 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5798 (t70) REVERT: K2 90 SER cc_start: 0.8800 (t) cc_final: 0.8513 (t) REVERT: L2 15 ASP cc_start: 0.7913 (m-30) cc_final: 0.7466 (m-30) REVERT: L2 43 ASP cc_start: 0.7412 (t0) cc_final: 0.7206 (t0) REVERT: L2 90 SER cc_start: 0.8837 (t) cc_final: 0.8569 (t) outliers start: 186 outliers final: 107 residues processed: 1488 average time/residue: 0.5369 time to fit residues: 1354.8239 Evaluate side-chains 1412 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1297 time to evaluate : 5.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 174 ASP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 140 ARG Chi-restraints excluded: chain B1 residue 256 THR Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 174 ASP Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 246 LEU Chi-restraints excluded: chain C1 residue 256 THR Chi-restraints excluded: chain C1 residue 279 THR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 256 THR Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 256 THR Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 279 THR Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 130 ASN Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 145 LYS Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 256 THR Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 174 ASP Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 256 THR Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 277 MET Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 131 ASN Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 88 THR Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 113 MET Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 82 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 82 SER Chi-restraints excluded: chain D2 residue 88 THR Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 82 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain F2 residue 113 MET Chi-restraints excluded: chain G2 residue 13 ASN Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 98 SER Chi-restraints excluded: chain H2 residue 5 ASP Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 80 SER Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 113 MET Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 88 THR Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 506 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 344 optimal weight: 0.0770 chunk 514 optimal weight: 0.7980 chunk 545 optimal weight: 0.9990 chunk 269 optimal weight: 0.4980 chunk 488 optimal weight: 0.1980 chunk 146 optimal weight: 7.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 82 ASN ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 82 ASN ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 311 ASN ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46356 Z= 0.192 Angle : 0.661 9.454 62520 Z= 0.337 Chirality : 0.042 0.139 6876 Planarity : 0.004 0.081 8064 Dihedral : 5.372 22.478 6336 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.54 % Allowed : 22.20 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5676 helix: -0.00 (0.10), residues: 2508 sheet: 1.02 (0.30), residues: 288 loop : -1.78 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPJ2 92 HIS 0.002 0.000 HISB1 155 PHE 0.026 0.001 PHEG1 190 TYR 0.023 0.002 TYRJ1 177 ARG 0.005 0.000 ARGE2 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1541 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1364 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8467 (m-40) cc_final: 0.8263 (m110) REVERT: A1 92 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7933 (tpp80) REVERT: A1 166 MET cc_start: 0.7889 (mtm) cc_final: 0.7458 (mtt) REVERT: B1 33 ASP cc_start: 0.7178 (t70) cc_final: 0.6833 (t0) REVERT: B1 259 GLN cc_start: 0.8923 (pt0) cc_final: 0.8679 (pt0) REVERT: B1 277 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8252 (tpt) REVERT: B1 350 ASP cc_start: 0.8854 (t0) cc_final: 0.8604 (t0) REVERT: C1 21 MET cc_start: 0.8374 (mmp) cc_final: 0.8142 (mmp) REVERT: C1 82 ASN cc_start: 0.8354 (m-40) cc_final: 0.8116 (m110) REVERT: C1 180 MET cc_start: 0.7683 (tpp) cc_final: 0.7136 (tpp) REVERT: C1 182 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8056 (mp0) REVERT: C1 272 LEU cc_start: 0.8982 (mt) cc_final: 0.8778 (mm) REVERT: C1 301 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7230 (mp0) REVERT: D1 21 MET cc_start: 0.8358 (mmt) cc_final: 0.8032 (mmt) REVERT: D1 36 MET cc_start: 0.7779 (mtm) cc_final: 0.7539 (ttm) REVERT: D1 76 LEU cc_start: 0.8617 (pt) cc_final: 0.8039 (pp) REVERT: D1 82 ASN cc_start: 0.8659 (m110) cc_final: 0.8181 (m110) REVERT: D1 122 PHE cc_start: 0.8686 (m-80) cc_final: 0.8357 (m-80) REVERT: D1 197 GLN cc_start: 0.8478 (tt0) cc_final: 0.8146 (tt0) REVERT: D1 269 ASN cc_start: 0.7931 (t0) cc_final: 0.7667 (t0) REVERT: D1 274 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7631 (tpp80) REVERT: D1 277 MET cc_start: 0.8408 (tpt) cc_final: 0.7874 (tpt) REVERT: D1 301 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7206 (mp0) REVERT: D1 350 ASP cc_start: 0.8860 (t0) cc_final: 0.8625 (t0) REVERT: E1 45 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: E1 87 MET cc_start: 0.8591 (tpp) cc_final: 0.8359 (tpp) REVERT: E1 166 MET cc_start: 0.7661 (mtm) cc_final: 0.7251 (mtt) REVERT: E1 171 GLU cc_start: 0.8262 (pt0) cc_final: 0.7771 (pt0) REVERT: E1 182 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7976 (mp0) REVERT: E1 217 TYR cc_start: 0.8113 (t80) cc_final: 0.7823 (t80) REVERT: E1 301 GLU cc_start: 0.7955 (mp0) cc_final: 0.7665 (mp0) REVERT: E1 316 TYR cc_start: 0.8469 (m-10) cc_final: 0.8176 (m-10) REVERT: E1 373 ASP cc_start: 0.7151 (t0) cc_final: 0.6925 (t0) REVERT: F1 79 HIS cc_start: 0.7495 (m-70) cc_final: 0.7039 (t-90) REVERT: F1 217 TYR cc_start: 0.8222 (t80) cc_final: 0.7829 (t80) REVERT: F1 274 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7684 (tpp80) REVERT: F1 316 TYR cc_start: 0.8738 (m-80) cc_final: 0.8212 (m-10) REVERT: F1 322 ASN cc_start: 0.8669 (t0) cc_final: 0.8389 (t0) REVERT: G1 21 MET cc_start: 0.8431 (mmt) cc_final: 0.8191 (mmt) REVERT: G1 82 ASN cc_start: 0.7474 (m-40) cc_final: 0.7190 (m110) REVERT: G1 277 MET cc_start: 0.8243 (tpt) cc_final: 0.7865 (tpt) REVERT: H1 73 LYS cc_start: 0.7778 (tptt) cc_final: 0.7305 (ttmm) REVERT: H1 128 LYS cc_start: 0.7104 (tppt) cc_final: 0.6422 (tptt) REVERT: H1 273 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7762 (mtt90) REVERT: H1 316 TYR cc_start: 0.8813 (m-80) cc_final: 0.8462 (m-10) REVERT: H1 330 LEU cc_start: 0.8509 (mm) cc_final: 0.8263 (mm) REVERT: I1 82 ASN cc_start: 0.8137 (m-40) cc_final: 0.7921 (m110) REVERT: I1 175 TYR cc_start: 0.7891 (m-80) cc_final: 0.7614 (m-80) REVERT: I1 269 ASN cc_start: 0.7999 (t0) cc_final: 0.7760 (t0) REVERT: I1 272 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8362 (mm) REVERT: I1 273 ARG cc_start: 0.7699 (mmm-85) cc_final: 0.7318 (mtt90) REVERT: J1 24 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7873 (p0) REVERT: J1 39 MET cc_start: 0.9149 (mtt) cc_final: 0.8811 (mtp) REVERT: J1 87 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7949 (tpp) REVERT: J1 166 MET cc_start: 0.7540 (mtm) cc_final: 0.7130 (mtt) REVERT: J1 180 MET cc_start: 0.8400 (tpp) cc_final: 0.7960 (tpp) REVERT: J1 272 LEU cc_start: 0.8862 (mt) cc_final: 0.8614 (mm) REVERT: J1 273 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7458 (mtt90) REVERT: J1 301 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7003 (mp0) REVERT: J1 316 TYR cc_start: 0.8493 (m-10) cc_final: 0.8200 (m-80) REVERT: K1 274 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7324 (tpp80) REVERT: K1 301 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7304 (mp0) REVERT: K1 326 GLU cc_start: 0.8282 (pp20) cc_final: 0.7786 (pp20) REVERT: L1 73 LYS cc_start: 0.7711 (tttp) cc_final: 0.7459 (ttmm) REVERT: L1 82 ASN cc_start: 0.8465 (m-40) cc_final: 0.8218 (m110) REVERT: L1 180 MET cc_start: 0.8406 (tpp) cc_final: 0.7793 (tpp) REVERT: L1 350 ASP cc_start: 0.8693 (t0) cc_final: 0.8394 (t0) REVERT: A2 15 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: A2 41 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5347 (t70) REVERT: A2 49 LEU cc_start: 0.9170 (mt) cc_final: 0.8938 (mt) REVERT: A2 90 SER cc_start: 0.8655 (t) cc_final: 0.8359 (t) REVERT: B2 15 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: B2 41 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5431 (t70) REVERT: B2 43 ASP cc_start: 0.7231 (t0) cc_final: 0.6665 (t70) REVERT: B2 90 SER cc_start: 0.8667 (t) cc_final: 0.8306 (t) REVERT: C2 15 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: C2 90 SER cc_start: 0.8659 (t) cc_final: 0.8373 (t) REVERT: C2 107 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: C2 117 PHE cc_start: 0.8221 (t80) cc_final: 0.7850 (t80) REVERT: D2 15 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: D2 41 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5215 (t70) REVERT: D2 61 TYR cc_start: 0.8735 (t80) cc_final: 0.8481 (t80) REVERT: D2 90 SER cc_start: 0.8669 (t) cc_final: 0.8385 (t) REVERT: E2 15 ASP cc_start: 0.7798 (m-30) cc_final: 0.7238 (m-30) REVERT: E2 41 ASP cc_start: 0.5743 (OUTLIER) cc_final: 0.5421 (t70) REVERT: E2 90 SER cc_start: 0.8673 (t) cc_final: 0.8286 (t) REVERT: F2 1 MET cc_start: 0.6319 (mmt) cc_final: 0.5039 (mmt) REVERT: F2 41 ASP cc_start: 0.5613 (OUTLIER) cc_final: 0.5276 (t70) REVERT: F2 90 SER cc_start: 0.8645 (t) cc_final: 0.8368 (t) REVERT: F2 107 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7636 (mtp) REVERT: G2 43 ASP cc_start: 0.7325 (t0) cc_final: 0.6828 (t70) REVERT: G2 90 SER cc_start: 0.8858 (t) cc_final: 0.8576 (t) REVERT: H2 15 ASP cc_start: 0.7772 (m-30) cc_final: 0.7447 (m-30) REVERT: H2 90 SER cc_start: 0.8712 (t) cc_final: 0.8436 (t) REVERT: I2 41 ASP cc_start: 0.5597 (OUTLIER) cc_final: 0.5263 (t70) REVERT: I2 90 SER cc_start: 0.8590 (t) cc_final: 0.8282 (t) REVERT: J2 15 ASP cc_start: 0.7801 (m-30) cc_final: 0.7547 (m-30) REVERT: J2 90 SER cc_start: 0.8807 (t) cc_final: 0.8522 (t) REVERT: K2 28 ASN cc_start: 0.8089 (t0) cc_final: 0.7658 (t0) REVERT: K2 41 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5566 (t70) REVERT: K2 43 ASP cc_start: 0.7415 (t0) cc_final: 0.7200 (t70) REVERT: K2 90 SER cc_start: 0.8622 (t) cc_final: 0.8337 (t) REVERT: L2 15 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: L2 28 ASN cc_start: 0.8147 (t0) cc_final: 0.7668 (t0) REVERT: L2 41 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.5320 (t70) REVERT: L2 90 SER cc_start: 0.8622 (t) cc_final: 0.8348 (t) REVERT: L2 107 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7677 (mtp) outliers start: 177 outliers final: 91 residues processed: 1448 average time/residue: 0.5155 time to fit residues: 1267.9938 Evaluate side-chains 1394 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1282 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 246 LEU Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 230 ILE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 94 VAL Chi-restraints excluded: chain G1 residue 103 ASP Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain H1 residue 32 SER Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 246 LEU Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 279 THR Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 126 ILE Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 82 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 454 optimal weight: 0.0970 chunk 309 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 405 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 465 optimal weight: 0.0050 chunk 376 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 489 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 82 ASN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 58 ASN ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 111 ASN ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2 111 ASN ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2 74 GLN ** H2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46356 Z= 0.202 Angle : 0.656 10.250 62520 Z= 0.332 Chirality : 0.042 0.207 6876 Planarity : 0.004 0.065 8064 Dihedral : 5.225 22.556 6336 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.48 % Allowed : 23.24 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.11), residues: 5676 helix: 0.03 (0.10), residues: 2520 sheet: 0.42 (0.31), residues: 312 loop : -1.78 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPG2 95 HIS 0.002 0.001 HISB1 155 PHE 0.024 0.001 PHEG1 190 TYR 0.020 0.002 TYRG1 177 ARG 0.005 0.000 ARGJ2 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1575 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1351 time to evaluate : 5.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 92 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7919 (tpp80) REVERT: A1 166 MET cc_start: 0.7834 (mtm) cc_final: 0.7421 (mtt) REVERT: B1 259 GLN cc_start: 0.8896 (pt0) cc_final: 0.8600 (pt0) REVERT: B1 301 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7383 (mp0) REVERT: B1 350 ASP cc_start: 0.8755 (t0) cc_final: 0.8412 (t0) REVERT: C1 82 ASN cc_start: 0.8368 (m-40) cc_final: 0.8105 (m110) REVERT: C1 182 GLU cc_start: 0.8813 (mm-30) cc_final: 0.7598 (mp0) REVERT: C1 197 GLN cc_start: 0.8479 (tt0) cc_final: 0.8228 (tt0) REVERT: C1 301 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7224 (mp0) REVERT: C1 326 GLU cc_start: 0.8109 (pp20) cc_final: 0.7884 (pp20) REVERT: D1 21 MET cc_start: 0.8381 (mmt) cc_final: 0.8100 (mmt) REVERT: D1 36 MET cc_start: 0.7787 (mtm) cc_final: 0.7465 (ttm) REVERT: D1 76 LEU cc_start: 0.8610 (pt) cc_final: 0.8253 (pp) REVERT: D1 82 ASN cc_start: 0.8655 (m110) cc_final: 0.8181 (m110) REVERT: D1 122 PHE cc_start: 0.8646 (m-80) cc_final: 0.8330 (m-80) REVERT: D1 182 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7951 (mp0) REVERT: D1 197 GLN cc_start: 0.8435 (tt0) cc_final: 0.8175 (tt0) REVERT: D1 269 ASN cc_start: 0.7944 (t0) cc_final: 0.7659 (t0) REVERT: D1 274 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7652 (tpp80) REVERT: D1 277 MET cc_start: 0.8421 (tpt) cc_final: 0.7883 (tpt) REVERT: D1 301 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7229 (mp0) REVERT: D1 373 ASP cc_start: 0.7167 (t0) cc_final: 0.6945 (t0) REVERT: E1 45 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8100 (ttm) REVERT: E1 76 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7685 (pp) REVERT: E1 79 HIS cc_start: 0.7527 (m-70) cc_final: 0.7118 (t-90) REVERT: E1 103 ASP cc_start: 0.7677 (m-30) cc_final: 0.7441 (m-30) REVERT: E1 166 MET cc_start: 0.7663 (mtm) cc_final: 0.7177 (mtt) REVERT: E1 171 GLU cc_start: 0.8252 (pt0) cc_final: 0.7718 (pt0) REVERT: E1 301 GLU cc_start: 0.7990 (mp0) cc_final: 0.7713 (mp0) REVERT: E1 316 TYR cc_start: 0.8512 (m-10) cc_final: 0.8183 (m-10) REVERT: E1 373 ASP cc_start: 0.7178 (t0) cc_final: 0.6973 (t0) REVERT: F1 79 HIS cc_start: 0.7518 (m-70) cc_final: 0.7184 (t-90) REVERT: F1 175 TYR cc_start: 0.8089 (m-80) cc_final: 0.7592 (m-80) REVERT: F1 176 TYR cc_start: 0.5468 (m-80) cc_final: 0.5267 (m-80) REVERT: F1 269 ASN cc_start: 0.7962 (t0) cc_final: 0.7650 (t0) REVERT: F1 274 ARG cc_start: 0.8457 (tpp80) cc_final: 0.7632 (tpp80) REVERT: F1 301 GLU cc_start: 0.7815 (mp0) cc_final: 0.7577 (mp0) REVERT: F1 316 TYR cc_start: 0.8723 (m-80) cc_final: 0.8140 (m-10) REVERT: F1 319 ASP cc_start: 0.8499 (m-30) cc_final: 0.8268 (m-30) REVERT: F1 322 ASN cc_start: 0.8654 (t0) cc_final: 0.8383 (t0) REVERT: F1 326 GLU cc_start: 0.8331 (pp20) cc_final: 0.7969 (pp20) REVERT: G1 82 ASN cc_start: 0.7563 (m-40) cc_final: 0.7259 (m110) REVERT: G1 182 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7568 (mp0) REVERT: G1 217 TYR cc_start: 0.8280 (t80) cc_final: 0.8060 (t80) REVERT: G1 277 MET cc_start: 0.8307 (tpt) cc_final: 0.8079 (tpt) REVERT: H1 45 MET cc_start: 0.8322 (mmm) cc_final: 0.8008 (ttm) REVERT: H1 73 LYS cc_start: 0.7763 (tptt) cc_final: 0.7284 (ttmm) REVERT: H1 82 ASN cc_start: 0.7668 (m-40) cc_final: 0.7462 (m110) REVERT: H1 128 LYS cc_start: 0.7106 (tppt) cc_final: 0.6435 (tptt) REVERT: H1 197 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: H1 273 ARG cc_start: 0.8024 (mmm-85) cc_final: 0.7740 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8832 (m-80) cc_final: 0.8452 (m-10) REVERT: H1 330 LEU cc_start: 0.8497 (mm) cc_final: 0.8230 (mm) REVERT: I1 88 LEU cc_start: 0.8937 (mp) cc_final: 0.8736 (mp) REVERT: I1 175 TYR cc_start: 0.7862 (m-80) cc_final: 0.7622 (m-80) REVERT: I1 182 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7781 (mp0) REVERT: I1 272 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8444 (mm) REVERT: I1 273 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7389 (mtt90) REVERT: I1 326 GLU cc_start: 0.8009 (pp20) cc_final: 0.7802 (pp20) REVERT: J1 24 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7902 (p0) REVERT: J1 87 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7960 (tpp) REVERT: J1 166 MET cc_start: 0.7633 (mtm) cc_final: 0.7249 (mtt) REVERT: J1 269 ASN cc_start: 0.7866 (t0) cc_final: 0.7661 (t0) REVERT: J1 301 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7036 (mp0) REVERT: K1 40 TYR cc_start: 0.9333 (t80) cc_final: 0.9029 (t80) REVERT: K1 48 ILE cc_start: 0.9507 (mm) cc_final: 0.9290 (tt) REVERT: K1 73 LYS cc_start: 0.7883 (tptt) cc_final: 0.7455 (ttmm) REVERT: K1 273 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7668 (mmm-85) REVERT: K1 301 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7290 (mp0) REVERT: K1 326 GLU cc_start: 0.8287 (pp20) cc_final: 0.7819 (pp20) REVERT: L1 73 LYS cc_start: 0.7699 (tttp) cc_final: 0.7462 (ttmm) REVERT: L1 175 TYR cc_start: 0.7727 (m-80) cc_final: 0.7396 (m-80) REVERT: L1 180 MET cc_start: 0.8393 (tpp) cc_final: 0.8099 (tpp) REVERT: L1 326 GLU cc_start: 0.7891 (pp20) cc_final: 0.7588 (pp20) REVERT: L1 350 ASP cc_start: 0.8511 (t0) cc_final: 0.8261 (t0) REVERT: A2 1 MET cc_start: 0.6153 (mmt) cc_final: 0.5404 (mmm) REVERT: A2 15 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: A2 41 ASP cc_start: 0.5540 (OUTLIER) cc_final: 0.5243 (t70) REVERT: A2 90 SER cc_start: 0.8632 (t) cc_final: 0.8361 (t) REVERT: B2 15 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: B2 41 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5428 (t70) REVERT: B2 61 TYR cc_start: 0.8766 (t80) cc_final: 0.8519 (t80) REVERT: B2 90 SER cc_start: 0.8768 (t) cc_final: 0.8505 (t) REVERT: C2 15 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: C2 90 SER cc_start: 0.8676 (t) cc_final: 0.8406 (t) REVERT: C2 107 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7479 (mtp) REVERT: D2 15 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: D2 41 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5115 (t70) REVERT: D2 90 SER cc_start: 0.8703 (t) cc_final: 0.8451 (t) REVERT: E2 15 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: E2 41 ASP cc_start: 0.5737 (OUTLIER) cc_final: 0.5419 (t70) REVERT: E2 61 TYR cc_start: 0.8686 (t80) cc_final: 0.8455 (t80) REVERT: E2 90 SER cc_start: 0.8733 (t) cc_final: 0.8466 (t) REVERT: F2 1 MET cc_start: 0.6310 (mmt) cc_final: 0.5530 (mmm) REVERT: F2 90 SER cc_start: 0.8676 (t) cc_final: 0.8379 (t) REVERT: F2 107 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7610 (mtp) REVERT: G2 41 ASP cc_start: 0.5849 (OUTLIER) cc_final: 0.5535 (t70) REVERT: G2 90 SER cc_start: 0.8841 (t) cc_final: 0.8532 (t) REVERT: H2 15 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: H2 28 ASN cc_start: 0.8037 (t0) cc_final: 0.7515 (t0) REVERT: H2 41 ASP cc_start: 0.5969 (OUTLIER) cc_final: 0.5662 (t70) REVERT: H2 61 TYR cc_start: 0.8767 (t80) cc_final: 0.8564 (t80) REVERT: H2 90 SER cc_start: 0.8711 (t) cc_final: 0.8444 (t) REVERT: I2 38 TYR cc_start: 0.7962 (t80) cc_final: 0.7756 (t80) REVERT: I2 41 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.5233 (t70) REVERT: I2 90 SER cc_start: 0.8592 (t) cc_final: 0.8310 (t) REVERT: J2 15 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7579 (m-30) REVERT: J2 41 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5719 (t70) REVERT: J2 90 SER cc_start: 0.8807 (t) cc_final: 0.8434 (t) REVERT: K2 28 ASN cc_start: 0.8100 (t0) cc_final: 0.7596 (t0) REVERT: K2 41 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5576 (t70) REVERT: K2 90 SER cc_start: 0.8625 (t) cc_final: 0.8360 (t) REVERT: L2 15 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: L2 28 ASN cc_start: 0.8118 (t0) cc_final: 0.7642 (t0) REVERT: L2 41 ASP cc_start: 0.5610 (OUTLIER) cc_final: 0.5301 (t70) REVERT: L2 90 SER cc_start: 0.8649 (t) cc_final: 0.8380 (t) REVERT: L2 107 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7718 (mtp) outliers start: 224 outliers final: 121 residues processed: 1473 average time/residue: 0.5151 time to fit residues: 1290.3222 Evaluate side-chains 1420 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1272 time to evaluate : 4.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 45 MET Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 153 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 246 LEU Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 279 THR Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 230 ILE Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 76 LEU Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 246 LEU Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 279 THR Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 103 ASP Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 141 TYR Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 94 VAL Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 94 VAL Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 279 THR Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 141 TYR Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 279 THR Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain E2 residue 113 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain J2 residue 106 LEU Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 183 optimal weight: 5.9990 chunk 490 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 545 optimal weight: 0.0770 chunk 452 optimal weight: 0.9980 chunk 252 optimal weight: 0.0040 chunk 45 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 82 ASN ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 82 ASN ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 111 ASN ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 111 ASN ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H2 111 ASN ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46356 Z= 0.200 Angle : 0.667 12.932 62520 Z= 0.334 Chirality : 0.043 0.201 6876 Planarity : 0.004 0.058 8064 Dihedral : 5.167 22.142 6336 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.68 % Allowed : 24.46 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 5676 helix: 0.08 (0.10), residues: 2520 sheet: 0.45 (0.31), residues: 312 loop : -1.78 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPJ2 92 HIS 0.002 0.000 HISL1 155 PHE 0.022 0.001 PHEG1 190 TYR 0.020 0.002 TYRB1 177 ARG 0.006 0.000 ARGG2 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1599 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1365 time to evaluate : 5.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8475 (m-40) cc_final: 0.8203 (m110) REVERT: A1 92 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7779 (tpp80) REVERT: A1 166 MET cc_start: 0.7801 (mtm) cc_final: 0.7354 (mtt) REVERT: A1 180 MET cc_start: 0.8179 (tpp) cc_final: 0.7494 (tpp) REVERT: B1 269 ASN cc_start: 0.7855 (t0) cc_final: 0.7620 (t0) REVERT: B1 350 ASP cc_start: 0.8637 (t0) cc_final: 0.8417 (t0) REVERT: C1 82 ASN cc_start: 0.8338 (m-40) cc_final: 0.8070 (m110) REVERT: C1 87 MET cc_start: 0.8434 (tpp) cc_final: 0.8230 (tpp) REVERT: C1 180 MET cc_start: 0.7708 (tpp) cc_final: 0.7255 (tpp) REVERT: C1 197 GLN cc_start: 0.8501 (tt0) cc_final: 0.8234 (tt0) REVERT: C1 373 ASP cc_start: 0.7019 (t0) cc_final: 0.6814 (t0) REVERT: D1 21 MET cc_start: 0.8435 (mmt) cc_final: 0.8065 (mmt) REVERT: D1 36 MET cc_start: 0.7767 (mtm) cc_final: 0.7547 (ttm) REVERT: D1 76 LEU cc_start: 0.8624 (pt) cc_final: 0.8269 (pp) REVERT: D1 122 PHE cc_start: 0.8602 (m-80) cc_final: 0.8339 (m-80) REVERT: D1 182 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8071 (mp0) REVERT: D1 197 GLN cc_start: 0.8452 (tt0) cc_final: 0.8211 (tt0) REVERT: D1 269 ASN cc_start: 0.7957 (t0) cc_final: 0.7637 (t0) REVERT: D1 301 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7186 (mp0) REVERT: E1 45 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.8022 (ttm) REVERT: E1 79 HIS cc_start: 0.7503 (m-70) cc_final: 0.7190 (t-90) REVERT: E1 87 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8279 (tpp) REVERT: E1 103 ASP cc_start: 0.7643 (m-30) cc_final: 0.7423 (m-30) REVERT: E1 166 MET cc_start: 0.7661 (mtm) cc_final: 0.7134 (mtt) REVERT: E1 171 GLU cc_start: 0.8232 (pt0) cc_final: 0.7719 (pt0) REVERT: E1 182 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7802 (mp0) REVERT: E1 197 GLN cc_start: 0.8466 (tt0) cc_final: 0.8197 (tt0) REVERT: E1 217 TYR cc_start: 0.8141 (t80) cc_final: 0.7868 (t80) REVERT: E1 301 GLU cc_start: 0.7990 (mp0) cc_final: 0.7725 (mp0) REVERT: E1 316 TYR cc_start: 0.8528 (m-10) cc_final: 0.8194 (m-10) REVERT: F1 79 HIS cc_start: 0.7426 (m-70) cc_final: 0.7224 (t-90) REVERT: F1 128 LYS cc_start: 0.7328 (ttmt) cc_final: 0.7049 (mmtp) REVERT: F1 175 TYR cc_start: 0.7913 (m-80) cc_final: 0.7588 (m-80) REVERT: F1 180 MET cc_start: 0.7638 (tpp) cc_final: 0.7232 (tpp) REVERT: F1 269 ASN cc_start: 0.7956 (t0) cc_final: 0.7735 (t0) REVERT: F1 301 GLU cc_start: 0.7789 (mp0) cc_final: 0.7513 (mp0) REVERT: F1 316 TYR cc_start: 0.8703 (m-80) cc_final: 0.8188 (m-10) REVERT: F1 319 ASP cc_start: 0.8476 (m-30) cc_final: 0.8274 (m-30) REVERT: F1 322 ASN cc_start: 0.8648 (t0) cc_final: 0.8426 (t0) REVERT: F1 326 GLU cc_start: 0.8290 (pp20) cc_final: 0.7944 (pp20) REVERT: G1 77 SER cc_start: 0.8815 (p) cc_final: 0.8518 (p) REVERT: G1 82 ASN cc_start: 0.7576 (m-40) cc_final: 0.7241 (m110) REVERT: G1 182 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7483 (mp0) REVERT: G1 274 ARG cc_start: 0.8450 (tpp80) cc_final: 0.7695 (tpp80) REVERT: H1 45 MET cc_start: 0.8285 (mmm) cc_final: 0.7589 (ttm) REVERT: H1 73 LYS cc_start: 0.7791 (tptt) cc_final: 0.7325 (ttmm) REVERT: H1 128 LYS cc_start: 0.6995 (tppt) cc_final: 0.6372 (tptt) REVERT: H1 197 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: H1 273 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8822 (m-80) cc_final: 0.8478 (m-10) REVERT: H1 330 LEU cc_start: 0.8541 (mm) cc_final: 0.8258 (mm) REVERT: I1 77 SER cc_start: 0.8691 (p) cc_final: 0.8325 (p) REVERT: I1 82 ASN cc_start: 0.7963 (m-40) cc_final: 0.7666 (m110) REVERT: I1 88 LEU cc_start: 0.8930 (mp) cc_final: 0.8681 (mp) REVERT: I1 182 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7732 (mp0) REVERT: I1 272 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8355 (mm) REVERT: I1 326 GLU cc_start: 0.8085 (pp20) cc_final: 0.7851 (pp20) REVERT: J1 24 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7875 (p0) REVERT: J1 39 MET cc_start: 0.9077 (mtt) cc_final: 0.8722 (mtp) REVERT: J1 87 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: J1 128 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6784 (mmtp) REVERT: J1 166 MET cc_start: 0.7648 (mtm) cc_final: 0.7224 (mtt) REVERT: J1 180 MET cc_start: 0.8490 (tpp) cc_final: 0.7948 (tpp) REVERT: J1 318 GLU cc_start: 0.8215 (tt0) cc_final: 0.7990 (tt0) REVERT: K1 40 TYR cc_start: 0.9341 (t80) cc_final: 0.9096 (t80) REVERT: K1 76 LEU cc_start: 0.8651 (pt) cc_final: 0.7995 (pp) REVERT: K1 326 GLU cc_start: 0.8242 (pp20) cc_final: 0.7804 (pp20) REVERT: L1 73 LYS cc_start: 0.7770 (tttp) cc_final: 0.7541 (ttmm) REVERT: L1 82 ASN cc_start: 0.8462 (m-40) cc_final: 0.8158 (m110) REVERT: L1 182 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: L1 197 GLN cc_start: 0.8538 (tt0) cc_final: 0.8199 (tt0) REVERT: L1 326 GLU cc_start: 0.7833 (pp20) cc_final: 0.7604 (pp20) REVERT: L1 350 ASP cc_start: 0.8436 (t0) cc_final: 0.8193 (t0) REVERT: A2 1 MET cc_start: 0.6063 (mmt) cc_final: 0.5358 (mmm) REVERT: A2 15 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: A2 41 ASP cc_start: 0.5365 (OUTLIER) cc_final: 0.5081 (t70) REVERT: A2 43 ASP cc_start: 0.7117 (t70) cc_final: 0.6747 (t70) REVERT: A2 90 SER cc_start: 0.8617 (t) cc_final: 0.8358 (t) REVERT: A2 107 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7713 (mtp) REVERT: B2 15 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: B2 41 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5335 (t70) REVERT: B2 61 TYR cc_start: 0.8732 (t80) cc_final: 0.8502 (t80) REVERT: B2 90 SER cc_start: 0.8732 (t) cc_final: 0.8469 (t) REVERT: C2 15 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: C2 41 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5394 (t70) REVERT: C2 90 SER cc_start: 0.8639 (t) cc_final: 0.8304 (t) REVERT: C2 107 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7448 (mtp) REVERT: D2 15 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: D2 41 ASP cc_start: 0.5524 (OUTLIER) cc_final: 0.5186 (t70) REVERT: D2 43 ASP cc_start: 0.7736 (t0) cc_final: 0.7517 (t70) REVERT: D2 61 TYR cc_start: 0.8724 (t80) cc_final: 0.8443 (t80) REVERT: D2 90 SER cc_start: 0.8657 (t) cc_final: 0.8414 (t) REVERT: E2 15 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: E2 41 ASP cc_start: 0.5721 (OUTLIER) cc_final: 0.5426 (t70) REVERT: E2 61 TYR cc_start: 0.8717 (t80) cc_final: 0.8517 (t80) REVERT: E2 90 SER cc_start: 0.8731 (t) cc_final: 0.8464 (t) REVERT: F2 1 MET cc_start: 0.6242 (mmt) cc_final: 0.5454 (mmm) REVERT: F2 41 ASP cc_start: 0.5544 (OUTLIER) cc_final: 0.5158 (t70) REVERT: F2 90 SER cc_start: 0.8626 (t) cc_final: 0.8346 (t) REVERT: F2 107 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7504 (mtp) REVERT: G2 41 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5416 (t70) REVERT: G2 43 ASP cc_start: 0.7248 (t0) cc_final: 0.6847 (t70) REVERT: G2 90 SER cc_start: 0.8928 (t) cc_final: 0.8657 (t) REVERT: H2 1 MET cc_start: 0.5649 (mmt) cc_final: 0.4704 (mmt) REVERT: H2 15 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: H2 28 ASN cc_start: 0.7942 (t0) cc_final: 0.7394 (t0) REVERT: H2 41 ASP cc_start: 0.5786 (OUTLIER) cc_final: 0.5474 (t70) REVERT: H2 90 SER cc_start: 0.8696 (t) cc_final: 0.8417 (t) REVERT: I2 28 ASN cc_start: 0.7939 (t0) cc_final: 0.7491 (t0) REVERT: I2 41 ASP cc_start: 0.5444 (OUTLIER) cc_final: 0.5155 (t70) REVERT: I2 90 SER cc_start: 0.8589 (t) cc_final: 0.8307 (t) REVERT: J2 15 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: J2 41 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5591 (t70) REVERT: J2 90 SER cc_start: 0.8918 (t) cc_final: 0.8650 (t) REVERT: K2 28 ASN cc_start: 0.8017 (t0) cc_final: 0.7518 (t0) REVERT: K2 41 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5532 (t70) REVERT: K2 90 SER cc_start: 0.8583 (t) cc_final: 0.8342 (t) REVERT: L2 15 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: L2 28 ASN cc_start: 0.8078 (t0) cc_final: 0.7543 (t0) REVERT: L2 41 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.5185 (t70) REVERT: L2 90 SER cc_start: 0.8596 (t) cc_final: 0.8335 (t) outliers start: 234 outliers final: 141 residues processed: 1493 average time/residue: 0.5282 time to fit residues: 1338.1533 Evaluate side-chains 1448 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1277 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 153 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain A1 residue 321 LEU Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 246 LEU Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain B1 residue 279 THR Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 78 LYS Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 230 ILE Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 279 THR Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 87 MET Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 371 LEU Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 246 LEU Chi-restraints excluded: chain F1 residue 279 THR Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 103 ASP Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 94 VAL Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 272 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 141 TYR Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 246 LEU Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 182 GLU Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 309 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 88 THR Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 526 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 398 optimal weight: 0.4980 chunk 308 optimal weight: 2.9990 chunk 459 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 543 optimal weight: 0.6980 chunk 340 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 chunk 250 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 82 ASN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 58 ASN ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 111 ASN ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46356 Z= 0.225 Angle : 0.691 13.104 62520 Z= 0.344 Chirality : 0.043 0.300 6876 Planarity : 0.004 0.055 8064 Dihedral : 5.159 21.945 6336 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.62 % Allowed : 25.36 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5676 helix: 0.11 (0.10), residues: 2508 sheet: 0.49 (0.31), residues: 312 loop : -1.77 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPG2 92 HIS 0.002 0.001 HISG2 53 PHE 0.023 0.001 PHEL1 190 TYR 0.023 0.002 TYRD2 34 ARG 0.007 0.000 ARGH2 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1574 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1343 time to evaluate : 5.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 33 ASP cc_start: 0.7462 (t70) cc_final: 0.7216 (t70) REVERT: B1 39 MET cc_start: 0.9300 (mtt) cc_final: 0.8986 (mtp) REVERT: B1 217 TYR cc_start: 0.8290 (t80) cc_final: 0.7806 (t80) REVERT: B1 269 ASN cc_start: 0.7941 (t0) cc_final: 0.7688 (t0) REVERT: B1 301 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7294 (mp0) REVERT: B1 350 ASP cc_start: 0.8621 (t0) cc_final: 0.8390 (t0) REVERT: C1 82 ASN cc_start: 0.8358 (m-40) cc_final: 0.8044 (m110) REVERT: C1 87 MET cc_start: 0.8416 (tpp) cc_final: 0.8150 (tpp) REVERT: C1 180 MET cc_start: 0.7872 (tpp) cc_final: 0.7407 (tpp) REVERT: C1 197 GLN cc_start: 0.8528 (tt0) cc_final: 0.8253 (tt0) REVERT: C1 220 LEU cc_start: 0.8935 (mm) cc_final: 0.8729 (mm) REVERT: C1 326 GLU cc_start: 0.8186 (pp20) cc_final: 0.7958 (pp20) REVERT: D1 21 MET cc_start: 0.8460 (mmt) cc_final: 0.8033 (mmt) REVERT: D1 36 MET cc_start: 0.7830 (mtm) cc_final: 0.7535 (ttm) REVERT: D1 76 LEU cc_start: 0.8635 (pt) cc_final: 0.8290 (pp) REVERT: D1 122 PHE cc_start: 0.8605 (m-80) cc_final: 0.8306 (m-80) REVERT: D1 182 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8112 (mp0) REVERT: D1 197 GLN cc_start: 0.8529 (tt0) cc_final: 0.8291 (tt0) REVERT: D1 269 ASN cc_start: 0.8038 (t0) cc_final: 0.7717 (t0) REVERT: D1 301 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7202 (mp0) REVERT: D1 373 ASP cc_start: 0.7028 (t0) cc_final: 0.6725 (t0) REVERT: E1 45 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8052 (ttm) REVERT: E1 79 HIS cc_start: 0.7544 (m-70) cc_final: 0.7224 (t-90) REVERT: E1 103 ASP cc_start: 0.7648 (m-30) cc_final: 0.7439 (m-30) REVERT: E1 166 MET cc_start: 0.7554 (mtm) cc_final: 0.7029 (mtt) REVERT: E1 171 GLU cc_start: 0.8269 (pt0) cc_final: 0.7771 (pt0) REVERT: E1 175 TYR cc_start: 0.7843 (m-80) cc_final: 0.7591 (m-80) REVERT: E1 182 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7883 (mp0) REVERT: E1 197 GLN cc_start: 0.8493 (tt0) cc_final: 0.8206 (tt0) REVERT: E1 301 GLU cc_start: 0.7934 (mp0) cc_final: 0.7695 (mp0) REVERT: E1 316 TYR cc_start: 0.8563 (m-10) cc_final: 0.8208 (m-10) REVERT: F1 79 HIS cc_start: 0.7439 (m-70) cc_final: 0.7195 (t-90) REVERT: F1 128 LYS cc_start: 0.7295 (ttmt) cc_final: 0.7046 (mmtp) REVERT: F1 162 PHE cc_start: 0.8411 (m-10) cc_final: 0.8210 (m-10) REVERT: F1 175 TYR cc_start: 0.7904 (m-80) cc_final: 0.7618 (m-80) REVERT: F1 180 MET cc_start: 0.7790 (tpp) cc_final: 0.7401 (tpp) REVERT: F1 220 LEU cc_start: 0.8861 (mm) cc_final: 0.8647 (mm) REVERT: F1 269 ASN cc_start: 0.7990 (t0) cc_final: 0.7642 (t0) REVERT: F1 301 GLU cc_start: 0.7790 (mp0) cc_final: 0.7570 (mp0) REVERT: F1 316 TYR cc_start: 0.8667 (m-80) cc_final: 0.8048 (m-10) REVERT: F1 322 ASN cc_start: 0.8654 (t0) cc_final: 0.8444 (t0) REVERT: F1 326 GLU cc_start: 0.8313 (pp20) cc_final: 0.7822 (pp20) REVERT: G1 21 MET cc_start: 0.8549 (mmt) cc_final: 0.7946 (mmt) REVERT: G1 77 SER cc_start: 0.8832 (p) cc_final: 0.8534 (p) REVERT: G1 82 ASN cc_start: 0.7639 (m-40) cc_final: 0.7272 (m110) REVERT: G1 171 GLU cc_start: 0.8261 (pt0) cc_final: 0.7723 (pt0) REVERT: G1 217 TYR cc_start: 0.8309 (t80) cc_final: 0.8106 (t80) REVERT: G1 326 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7812 (pp20) REVERT: H1 82 ASN cc_start: 0.7802 (m-40) cc_final: 0.7532 (m110) REVERT: H1 182 GLU cc_start: 0.8755 (mm-30) cc_final: 0.7524 (mp0) REVERT: H1 197 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: H1 273 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8828 (m-80) cc_final: 0.8453 (m-10) REVERT: I1 45 MET cc_start: 0.8342 (mmm) cc_final: 0.8130 (ttm) REVERT: I1 82 ASN cc_start: 0.8081 (m-40) cc_final: 0.7849 (m110) REVERT: I1 88 LEU cc_start: 0.8986 (mp) cc_final: 0.8752 (mp) REVERT: I1 182 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7732 (mp0) REVERT: I1 373 ASP cc_start: 0.6625 (t0) cc_final: 0.6252 (t0) REVERT: J1 24 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7816 (p0) REVERT: J1 39 MET cc_start: 0.9081 (mtt) cc_final: 0.8712 (mtp) REVERT: J1 87 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8056 (tpp) REVERT: J1 166 MET cc_start: 0.7688 (mtm) cc_final: 0.7276 (mtt) REVERT: J1 180 MET cc_start: 0.8531 (tpp) cc_final: 0.7954 (tpp) REVERT: J1 273 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7619 (mtt180) REVERT: J1 318 GLU cc_start: 0.8237 (tt0) cc_final: 0.8026 (tt0) REVERT: K1 21 MET cc_start: 0.8467 (mmt) cc_final: 0.8048 (mmt) REVERT: K1 39 MET cc_start: 0.9209 (mtt) cc_final: 0.8902 (mtp) REVERT: K1 40 TYR cc_start: 0.9368 (t80) cc_final: 0.9153 (t80) REVERT: K1 76 LEU cc_start: 0.8682 (pt) cc_final: 0.8003 (pp) REVERT: K1 326 GLU cc_start: 0.8262 (pp20) cc_final: 0.7804 (pp20) REVERT: L1 73 LYS cc_start: 0.7820 (tttp) cc_final: 0.7604 (ttmm) REVERT: L1 182 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: L1 197 GLN cc_start: 0.8529 (tt0) cc_final: 0.8144 (tt0) REVERT: L1 326 GLU cc_start: 0.7799 (pp20) cc_final: 0.7541 (pp20) REVERT: L1 350 ASP cc_start: 0.8452 (t0) cc_final: 0.8214 (t0) REVERT: A2 1 MET cc_start: 0.5993 (mmt) cc_final: 0.5302 (mmm) REVERT: A2 15 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: A2 41 ASP cc_start: 0.5447 (OUTLIER) cc_final: 0.5142 (t70) REVERT: A2 43 ASP cc_start: 0.7134 (t70) cc_final: 0.6883 (t70) REVERT: A2 90 SER cc_start: 0.8742 (t) cc_final: 0.8493 (t) REVERT: A2 107 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: B2 15 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: B2 28 ASN cc_start: 0.7863 (t0) cc_final: 0.7432 (t0) REVERT: B2 41 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5355 (t70) REVERT: B2 61 TYR cc_start: 0.8735 (t80) cc_final: 0.8525 (t80) REVERT: B2 90 SER cc_start: 0.8769 (t) cc_final: 0.8511 (t) REVERT: C2 15 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: C2 41 ASP cc_start: 0.5820 (OUTLIER) cc_final: 0.5510 (t70) REVERT: C2 49 LEU cc_start: 0.9218 (mm) cc_final: 0.8961 (mm) REVERT: C2 90 SER cc_start: 0.8705 (t) cc_final: 0.8465 (t) REVERT: C2 107 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7454 (mtp) REVERT: D2 15 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: D2 34 TYR cc_start: 0.8562 (t80) cc_final: 0.8123 (t80) REVERT: D2 41 ASP cc_start: 0.5650 (OUTLIER) cc_final: 0.5287 (t70) REVERT: D2 43 ASP cc_start: 0.7648 (t0) cc_final: 0.7032 (t70) REVERT: D2 90 SER cc_start: 0.8754 (t) cc_final: 0.8489 (t) REVERT: E2 15 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: E2 41 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5508 (t70) REVERT: E2 61 TYR cc_start: 0.8715 (t80) cc_final: 0.8507 (t80) REVERT: E2 90 SER cc_start: 0.8753 (t) cc_final: 0.8498 (t) REVERT: E2 107 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7659 (mtp) REVERT: F2 1 MET cc_start: 0.6215 (mmt) cc_final: 0.5438 (mmm) REVERT: F2 41 ASP cc_start: 0.5696 (OUTLIER) cc_final: 0.5325 (t70) REVERT: F2 90 SER cc_start: 0.8688 (t) cc_final: 0.8428 (t) REVERT: F2 107 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7522 (mtp) REVERT: G2 41 ASP cc_start: 0.5716 (OUTLIER) cc_final: 0.5392 (t70) REVERT: G2 43 ASP cc_start: 0.7307 (t0) cc_final: 0.7029 (t70) REVERT: G2 90 SER cc_start: 0.8968 (t) cc_final: 0.8721 (t) REVERT: H2 1 MET cc_start: 0.5615 (mmt) cc_final: 0.4677 (mmt) REVERT: H2 15 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: H2 28 ASN cc_start: 0.7927 (t0) cc_final: 0.7410 (t0) REVERT: H2 41 ASP cc_start: 0.5886 (OUTLIER) cc_final: 0.5565 (t70) REVERT: H2 61 TYR cc_start: 0.8758 (t80) cc_final: 0.8542 (t80) REVERT: H2 90 SER cc_start: 0.8740 (t) cc_final: 0.8478 (t) REVERT: I2 28 ASN cc_start: 0.7970 (t0) cc_final: 0.7525 (t0) REVERT: I2 41 ASP cc_start: 0.5546 (OUTLIER) cc_final: 0.5237 (t70) REVERT: I2 90 SER cc_start: 0.8682 (t) cc_final: 0.8403 (t) REVERT: J2 15 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: J2 41 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5791 (t70) REVERT: J2 90 SER cc_start: 0.8901 (t) cc_final: 0.8671 (t) REVERT: K2 28 ASN cc_start: 0.7966 (t0) cc_final: 0.7456 (t0) REVERT: K2 41 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5571 (t70) REVERT: K2 90 SER cc_start: 0.8627 (t) cc_final: 0.8371 (t) REVERT: L2 15 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: L2 28 ASN cc_start: 0.8132 (t0) cc_final: 0.7579 (t0) REVERT: L2 41 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.5299 (t70) REVERT: L2 90 SER cc_start: 0.8677 (t) cc_final: 0.8403 (t) outliers start: 231 outliers final: 175 residues processed: 1476 average time/residue: 0.5250 time to fit residues: 1323.4662 Evaluate side-chains 1494 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1290 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 78 LYS Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 153 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain A1 residue 321 LEU Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 246 LEU Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 78 LYS Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 140 ARG Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 230 ILE Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain E1 residue 371 LEU Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 126 ILE Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 246 LEU Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 78 LYS Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 24 ASN Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 94 VAL Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain H1 residue 371 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 78 LYS Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 141 TYR Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 246 LEU Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 321 LEU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 182 GLU Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain L1 residue 309 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 88 THR Chi-restraints excluded: chain A2 residue 91 ASP Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 84 VAL Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 5 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 64 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 336 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 106 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 345 optimal weight: 0.6980 chunk 370 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 53 HIS B2 53 HIS ** C2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 53 HIS E2 53 HIS ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J2 53 HIS ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46356 Z= 0.271 Angle : 0.725 14.487 62520 Z= 0.360 Chirality : 0.045 0.349 6876 Planarity : 0.004 0.054 8064 Dihedral : 5.267 25.287 6336 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.06 % Allowed : 25.78 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.11), residues: 5676 helix: 0.07 (0.10), residues: 2508 sheet: 0.47 (0.31), residues: 312 loop : -1.77 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPH1 361 HIS 0.003 0.001 HISG2 53 PHE 0.021 0.002 PHEK1 190 TYR 0.030 0.002 TYRJ1 217 ARG 0.007 0.000 ARGB2 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1596 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1343 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 180 MET cc_start: 0.8304 (tpp) cc_final: 0.7781 (tpp) REVERT: B1 39 MET cc_start: 0.9281 (mtt) cc_final: 0.8940 (mtp) REVERT: B1 217 TYR cc_start: 0.8318 (t80) cc_final: 0.8000 (t80) REVERT: B1 269 ASN cc_start: 0.8008 (t0) cc_final: 0.7708 (t0) REVERT: B1 350 ASP cc_start: 0.8670 (t0) cc_final: 0.8386 (t0) REVERT: C1 25 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7379 (ptm-80) REVERT: C1 45 MET cc_start: 0.8275 (mmm) cc_final: 0.7683 (tpp) REVERT: C1 76 LEU cc_start: 0.8710 (pt) cc_final: 0.8475 (pp) REVERT: C1 82 ASN cc_start: 0.8415 (m-40) cc_final: 0.8054 (m110) REVERT: C1 197 GLN cc_start: 0.8507 (tt0) cc_final: 0.8235 (tt0) REVERT: D1 21 MET cc_start: 0.8506 (mmt) cc_final: 0.8044 (mmt) REVERT: D1 36 MET cc_start: 0.7836 (mtm) cc_final: 0.7540 (ttm) REVERT: D1 122 PHE cc_start: 0.8640 (m-80) cc_final: 0.8377 (m-80) REVERT: D1 182 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8234 (mp0) REVERT: D1 197 GLN cc_start: 0.8520 (tt0) cc_final: 0.8300 (tt0) REVERT: D1 269 ASN cc_start: 0.8076 (t0) cc_final: 0.7757 (t0) REVERT: D1 301 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7238 (mp0) REVERT: D1 326 GLU cc_start: 0.8182 (pp20) cc_final: 0.7733 (pp20) REVERT: D1 373 ASP cc_start: 0.6974 (t0) cc_final: 0.6686 (t0) REVERT: E1 25 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7317 (ptm-80) REVERT: E1 45 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8111 (ttm) REVERT: E1 87 MET cc_start: 0.8616 (tpp) cc_final: 0.8409 (tpp) REVERT: E1 103 ASP cc_start: 0.7701 (m-30) cc_final: 0.7494 (m-30) REVERT: E1 171 GLU cc_start: 0.8264 (pt0) cc_final: 0.7755 (pt0) REVERT: E1 175 TYR cc_start: 0.7768 (m-80) cc_final: 0.7336 (m-80) REVERT: E1 180 MET cc_start: 0.7988 (tpp) cc_final: 0.7514 (tpp) REVERT: E1 182 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7916 (mp0) REVERT: E1 197 GLN cc_start: 0.8488 (tt0) cc_final: 0.8112 (tt0) REVERT: E1 274 ARG cc_start: 0.8561 (tpp80) cc_final: 0.7829 (tpp80) REVERT: E1 301 GLU cc_start: 0.7920 (mp0) cc_final: 0.7695 (mp0) REVERT: E1 316 TYR cc_start: 0.8606 (m-10) cc_final: 0.8220 (m-10) REVERT: F1 25 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7350 (ptt90) REVERT: F1 128 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6737 (mmtp) REVERT: F1 175 TYR cc_start: 0.8068 (m-80) cc_final: 0.7628 (m-80) REVERT: F1 220 LEU cc_start: 0.8873 (mm) cc_final: 0.8670 (mm) REVERT: F1 301 GLU cc_start: 0.7811 (mp0) cc_final: 0.7602 (mp0) REVERT: F1 316 TYR cc_start: 0.8685 (m-80) cc_final: 0.8002 (m-10) REVERT: F1 322 ASN cc_start: 0.8660 (t0) cc_final: 0.8420 (t0) REVERT: F1 326 GLU cc_start: 0.8339 (pp20) cc_final: 0.7776 (pp20) REVERT: G1 21 MET cc_start: 0.8578 (mmt) cc_final: 0.7931 (mmt) REVERT: G1 82 ASN cc_start: 0.7840 (m-40) cc_final: 0.7425 (m110) REVERT: G1 171 GLU cc_start: 0.8288 (pt0) cc_final: 0.7746 (pt0) REVERT: G1 180 MET cc_start: 0.8342 (tpp) cc_final: 0.7902 (tpp) REVERT: H1 35 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8524 (mt-10) REVERT: H1 76 LEU cc_start: 0.8467 (pt) cc_final: 0.8265 (pp) REVERT: H1 187 TYR cc_start: 0.8426 (t80) cc_final: 0.8105 (t80) REVERT: H1 197 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: H1 217 TYR cc_start: 0.8273 (t80) cc_final: 0.8000 (t80) REVERT: H1 273 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8845 (m-80) cc_final: 0.8447 (m-10) REVERT: I1 82 ASN cc_start: 0.8131 (m-40) cc_final: 0.7905 (m110) REVERT: I1 88 LEU cc_start: 0.9064 (mp) cc_final: 0.8816 (mp) REVERT: I1 175 TYR cc_start: 0.8001 (m-80) cc_final: 0.7352 (m-80) REVERT: I1 182 GLU cc_start: 0.8718 (mm-30) cc_final: 0.7797 (mp0) REVERT: I1 269 ASN cc_start: 0.8118 (t0) cc_final: 0.7810 (t0) REVERT: I1 373 ASP cc_start: 0.6748 (t0) cc_final: 0.6493 (t0) REVERT: J1 24 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7811 (p0) REVERT: J1 76 LEU cc_start: 0.8600 (pt) cc_final: 0.8236 (pp) REVERT: J1 87 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (tpp) REVERT: J1 166 MET cc_start: 0.7705 (mtm) cc_final: 0.7339 (mtt) REVERT: J1 180 MET cc_start: 0.8654 (tpp) cc_final: 0.8019 (tpp) REVERT: J1 218 LYS cc_start: 0.8589 (tppt) cc_final: 0.8261 (mmmm) REVERT: J1 273 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7697 (mtt180) REVERT: K1 40 TYR cc_start: 0.9402 (t80) cc_final: 0.9143 (t80) REVERT: K1 273 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: K1 274 ARG cc_start: 0.8555 (tpp80) cc_final: 0.7624 (tpp80) REVERT: K1 326 GLU cc_start: 0.8322 (pp20) cc_final: 0.7842 (pp20) REVERT: L1 73 LYS cc_start: 0.7817 (tttp) cc_final: 0.7598 (ttmm) REVERT: L1 82 ASN cc_start: 0.8414 (m-40) cc_final: 0.8103 (m110) REVERT: L1 182 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: L1 197 GLN cc_start: 0.8603 (tt0) cc_final: 0.8235 (tt0) REVERT: L1 326 GLU cc_start: 0.7804 (pp20) cc_final: 0.7548 (pp20) REVERT: L1 350 ASP cc_start: 0.8547 (t0) cc_final: 0.8276 (t0) REVERT: A2 1 MET cc_start: 0.5829 (mmt) cc_final: 0.5309 (mmm) REVERT: A2 15 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: A2 41 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5304 (t70) REVERT: A2 90 SER cc_start: 0.8852 (t) cc_final: 0.8606 (t) REVERT: A2 107 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: B2 15 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7311 (m-30) REVERT: B2 28 ASN cc_start: 0.7851 (t0) cc_final: 0.7397 (t0) REVERT: B2 41 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5526 (t70) REVERT: B2 90 SER cc_start: 0.8874 (t) cc_final: 0.8611 (t) REVERT: C2 15 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: C2 28 ASN cc_start: 0.7907 (t0) cc_final: 0.7358 (t0) REVERT: C2 41 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5559 (t70) REVERT: C2 90 SER cc_start: 0.8819 (t) cc_final: 0.8570 (t) REVERT: C2 107 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7570 (mtp) REVERT: C2 117 PHE cc_start: 0.8267 (t80) cc_final: 0.7963 (t80) REVERT: D2 15 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: D2 34 TYR cc_start: 0.8674 (t80) cc_final: 0.8399 (t80) REVERT: D2 41 ASP cc_start: 0.5782 (OUTLIER) cc_final: 0.5421 (t70) REVERT: D2 90 SER cc_start: 0.8846 (t) cc_final: 0.8607 (t) REVERT: E2 15 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: E2 41 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.5543 (t70) REVERT: E2 90 SER cc_start: 0.8861 (t) cc_final: 0.8606 (t) REVERT: E2 107 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: F2 1 MET cc_start: 0.6245 (mmt) cc_final: 0.5607 (mmm) REVERT: F2 41 ASP cc_start: 0.5794 (OUTLIER) cc_final: 0.5401 (t70) REVERT: F2 90 SER cc_start: 0.8832 (t) cc_final: 0.8592 (t) REVERT: F2 107 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7587 (mtp) REVERT: G2 41 ASP cc_start: 0.5825 (OUTLIER) cc_final: 0.5445 (t70) REVERT: G2 90 SER cc_start: 0.9028 (t) cc_final: 0.8788 (t) REVERT: H2 15 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: H2 28 ASN cc_start: 0.7983 (t0) cc_final: 0.7441 (t0) REVERT: H2 41 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5617 (t70) REVERT: H2 61 TYR cc_start: 0.8745 (t80) cc_final: 0.8526 (t80) REVERT: H2 90 SER cc_start: 0.8835 (t) cc_final: 0.8554 (t) REVERT: I2 28 ASN cc_start: 0.7951 (t0) cc_final: 0.7474 (t0) REVERT: I2 41 ASP cc_start: 0.5669 (OUTLIER) cc_final: 0.5363 (t70) REVERT: I2 90 SER cc_start: 0.8835 (t) cc_final: 0.8552 (t) REVERT: J2 15 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: J2 41 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5756 (t70) REVERT: J2 90 SER cc_start: 0.8929 (t) cc_final: 0.8696 (t) REVERT: K2 28 ASN cc_start: 0.7923 (t0) cc_final: 0.7369 (t0) REVERT: K2 41 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5523 (t70) REVERT: K2 90 SER cc_start: 0.8742 (t) cc_final: 0.8470 (t) REVERT: L2 15 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: L2 28 ASN cc_start: 0.8196 (t0) cc_final: 0.7605 (t0) REVERT: L2 41 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5245 (t70) REVERT: L2 90 SER cc_start: 0.8824 (t) cc_final: 0.8555 (t) REVERT: L2 107 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7760 (mtp) outliers start: 253 outliers final: 188 residues processed: 1483 average time/residue: 0.5280 time to fit residues: 1323.4503 Evaluate side-chains 1511 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1293 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 78 LYS Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 277 MET Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain A1 residue 321 LEU Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 163 THR Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 24 ASN Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 78 LYS Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 163 THR Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain E1 residue 45 MET Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 126 ILE Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 78 LYS Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 163 THR Chi-restraints excluded: chain G1 residue 174 ASP Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 24 ASN Chi-restraints excluded: chain H1 residue 32 SER Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 157 THR Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain H1 residue 371 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 163 THR Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 256 THR Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 149 ILE Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 163 THR Chi-restraints excluded: chain L1 residue 182 GLU Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain L1 residue 309 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 88 THR Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 64 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 88 THR Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain C2 residue 113 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 84 VAL Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 38 TYR Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 64 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 494 optimal weight: 0.9980 chunk 520 optimal weight: 0.9990 chunk 475 optimal weight: 0.6980 chunk 506 optimal weight: 0.5980 chunk 304 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 397 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 457 optimal weight: 1.9990 chunk 479 optimal weight: 2.9990 chunk 504 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1 82 ASN ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 82 ASN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 82 ASN ** J1 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 53 HIS ** E2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 53 HIS ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 46356 Z= 0.232 Angle : 0.728 13.200 62520 Z= 0.358 Chirality : 0.045 0.375 6876 Planarity : 0.004 0.053 8064 Dihedral : 5.243 24.191 6336 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.84 % Allowed : 26.44 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5676 helix: 0.04 (0.10), residues: 2508 sheet: 0.46 (0.31), residues: 312 loop : -1.76 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPG2 92 HIS 0.003 0.001 HISE2 53 PHE 0.023 0.001 PHEB1 190 TYR 0.033 0.002 TYRJ1 217 ARG 0.007 0.000 ARGB2 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1314 time to evaluate : 6.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 82 ASN cc_start: 0.8383 (m-40) cc_final: 0.8134 (m110) REVERT: A1 166 MET cc_start: 0.7678 (mtm) cc_final: 0.7337 (mtt) REVERT: A1 180 MET cc_start: 0.8167 (tpp) cc_final: 0.7413 (tpp) REVERT: A1 301 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7313 (mp0) REVERT: B1 36 MET cc_start: 0.7822 (ttm) cc_final: 0.7557 (ttm) REVERT: B1 39 MET cc_start: 0.9272 (mtt) cc_final: 0.8908 (mtp) REVERT: B1 269 ASN cc_start: 0.8006 (t0) cc_final: 0.7711 (t0) REVERT: B1 301 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7342 (mp0) REVERT: B1 350 ASP cc_start: 0.8638 (t0) cc_final: 0.8364 (t0) REVERT: C1 25 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7344 (ptm-80) REVERT: C1 45 MET cc_start: 0.8227 (mmm) cc_final: 0.7594 (tpp) REVERT: C1 76 LEU cc_start: 0.8659 (pt) cc_final: 0.8415 (pp) REVERT: C1 82 ASN cc_start: 0.8390 (m-40) cc_final: 0.8024 (m110) REVERT: C1 180 MET cc_start: 0.7947 (tpp) cc_final: 0.7494 (tpp) REVERT: C1 197 GLN cc_start: 0.8507 (tt0) cc_final: 0.8247 (tt0) REVERT: C1 220 LEU cc_start: 0.8946 (mm) cc_final: 0.8736 (mm) REVERT: D1 21 MET cc_start: 0.8480 (mmt) cc_final: 0.7988 (mmt) REVERT: D1 36 MET cc_start: 0.7802 (mtm) cc_final: 0.7506 (ttm) REVERT: D1 122 PHE cc_start: 0.8618 (m-80) cc_final: 0.8318 (m-80) REVERT: D1 182 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8248 (mp0) REVERT: D1 197 GLN cc_start: 0.8538 (tt0) cc_final: 0.8319 (tt0) REVERT: D1 269 ASN cc_start: 0.8042 (t0) cc_final: 0.7714 (t0) REVERT: D1 301 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7173 (mp0) REVERT: D1 326 GLU cc_start: 0.8172 (pp20) cc_final: 0.7728 (pp20) REVERT: D1 373 ASP cc_start: 0.6937 (t0) cc_final: 0.6662 (t0) REVERT: E1 25 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7308 (ptm-80) REVERT: E1 166 MET cc_start: 0.7485 (mtm) cc_final: 0.7055 (mtt) REVERT: E1 171 GLU cc_start: 0.8223 (pt0) cc_final: 0.7737 (pt0) REVERT: E1 175 TYR cc_start: 0.7604 (m-80) cc_final: 0.7274 (m-80) REVERT: E1 180 MET cc_start: 0.7926 (tpp) cc_final: 0.7707 (tpp) REVERT: E1 182 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7896 (mp0) REVERT: E1 197 GLN cc_start: 0.8498 (tt0) cc_final: 0.8178 (tt0) REVERT: E1 274 ARG cc_start: 0.8543 (tpp80) cc_final: 0.7850 (tpp80) REVERT: E1 316 TYR cc_start: 0.8622 (m-10) cc_final: 0.8255 (m-10) REVERT: F1 25 ARG cc_start: 0.8124 (mtt-85) cc_final: 0.7344 (ptt90) REVERT: F1 45 MET cc_start: 0.8428 (mmm) cc_final: 0.7778 (ttm) REVERT: F1 128 LYS cc_start: 0.7283 (ttmt) cc_final: 0.6737 (mmtp) REVERT: F1 175 TYR cc_start: 0.7851 (m-80) cc_final: 0.7522 (m-80) REVERT: F1 269 ASN cc_start: 0.8070 (t0) cc_final: 0.7740 (t0) REVERT: F1 316 TYR cc_start: 0.8633 (m-80) cc_final: 0.8026 (m-10) REVERT: G1 21 MET cc_start: 0.8563 (mmt) cc_final: 0.7907 (mmt) REVERT: G1 45 MET cc_start: 0.8271 (mmm) cc_final: 0.7907 (ttm) REVERT: G1 77 SER cc_start: 0.8828 (p) cc_final: 0.8525 (p) REVERT: G1 82 ASN cc_start: 0.7877 (m-40) cc_final: 0.7432 (m110) REVERT: G1 171 GLU cc_start: 0.8290 (pt0) cc_final: 0.7798 (pt0) REVERT: G1 180 MET cc_start: 0.8137 (tpp) cc_final: 0.7740 (tpp) REVERT: G1 326 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7806 (pp20) REVERT: H1 45 MET cc_start: 0.8276 (mmm) cc_final: 0.8015 (ttm) REVERT: H1 82 ASN cc_start: 0.7966 (m-40) cc_final: 0.7681 (m110) REVERT: H1 182 GLU cc_start: 0.8781 (mm-30) cc_final: 0.7598 (mp0) REVERT: H1 197 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: H1 273 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8823 (m-80) cc_final: 0.8452 (m-10) REVERT: I1 45 MET cc_start: 0.8378 (mmm) cc_final: 0.7948 (ttm) REVERT: I1 82 ASN cc_start: 0.8142 (m-40) cc_final: 0.7905 (m110) REVERT: I1 88 LEU cc_start: 0.9013 (mp) cc_final: 0.8730 (mp) REVERT: I1 269 ASN cc_start: 0.8060 (t0) cc_final: 0.7750 (t0) REVERT: I1 328 PHE cc_start: 0.8303 (m-10) cc_final: 0.8103 (m-80) REVERT: I1 373 ASP cc_start: 0.6740 (t0) cc_final: 0.6525 (t0) REVERT: J1 39 MET cc_start: 0.9049 (mtt) cc_final: 0.8677 (mtp) REVERT: J1 76 LEU cc_start: 0.8567 (pt) cc_final: 0.8173 (pp) REVERT: J1 82 ASN cc_start: 0.8198 (m-40) cc_final: 0.7942 (m110) REVERT: J1 87 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (tpp) REVERT: J1 116 LEU cc_start: 0.8536 (mt) cc_final: 0.8246 (pp) REVERT: J1 166 MET cc_start: 0.7743 (mtm) cc_final: 0.7361 (mtt) REVERT: J1 180 MET cc_start: 0.8509 (tpp) cc_final: 0.7909 (tpp) REVERT: J1 218 LYS cc_start: 0.8503 (tppt) cc_final: 0.8286 (mmmm) REVERT: J1 273 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7663 (mtt180) REVERT: K1 21 MET cc_start: 0.8444 (mmt) cc_final: 0.7920 (mmt) REVERT: K1 273 ARG cc_start: 0.7993 (mmm-85) cc_final: 0.7518 (mmm-85) REVERT: K1 274 ARG cc_start: 0.8498 (tpp80) cc_final: 0.7569 (tpp80) REVERT: K1 326 GLU cc_start: 0.8278 (pp20) cc_final: 0.7787 (pp20) REVERT: L1 73 LYS cc_start: 0.7846 (tttp) cc_final: 0.7638 (ttmm) REVERT: L1 82 ASN cc_start: 0.8324 (m-40) cc_final: 0.8098 (m110) REVERT: L1 182 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8511 (tp30) REVERT: L1 197 GLN cc_start: 0.8594 (tt0) cc_final: 0.8245 (tt0) REVERT: L1 326 GLU cc_start: 0.7806 (pp20) cc_final: 0.7534 (pp20) REVERT: L1 350 ASP cc_start: 0.8475 (t0) cc_final: 0.8244 (t0) REVERT: A2 1 MET cc_start: 0.5838 (mmt) cc_final: 0.5306 (mmm) REVERT: A2 15 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: A2 41 ASP cc_start: 0.5528 (OUTLIER) cc_final: 0.5214 (t70) REVERT: A2 90 SER cc_start: 0.8779 (t) cc_final: 0.8527 (t) REVERT: A2 107 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7649 (mtp) REVERT: B2 15 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: B2 28 ASN cc_start: 0.7780 (t0) cc_final: 0.7328 (t0) REVERT: B2 41 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5445 (t70) REVERT: B2 61 TYR cc_start: 0.8794 (t80) cc_final: 0.8563 (t80) REVERT: B2 90 SER cc_start: 0.8799 (t) cc_final: 0.8540 (t) REVERT: C2 15 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: C2 28 ASN cc_start: 0.7888 (t0) cc_final: 0.7364 (t0) REVERT: C2 41 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.5561 (t70) REVERT: C2 90 SER cc_start: 0.8728 (t) cc_final: 0.8482 (t) REVERT: C2 107 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7454 (mtp) REVERT: C2 117 PHE cc_start: 0.8158 (t80) cc_final: 0.7920 (t80) REVERT: D2 15 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: D2 34 TYR cc_start: 0.8643 (t80) cc_final: 0.8418 (t80) REVERT: D2 41 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5418 (t70) REVERT: D2 61 TYR cc_start: 0.8779 (t80) cc_final: 0.8450 (t80) REVERT: D2 90 SER cc_start: 0.8718 (t) cc_final: 0.8457 (t) REVERT: E2 5 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7617 (t70) REVERT: E2 15 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: E2 28 ASN cc_start: 0.7660 (t0) cc_final: 0.7170 (t0) REVERT: E2 41 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5507 (t70) REVERT: E2 61 TYR cc_start: 0.8799 (t80) cc_final: 0.8561 (t80) REVERT: E2 90 SER cc_start: 0.8767 (t) cc_final: 0.8507 (t) REVERT: E2 107 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: F2 1 MET cc_start: 0.6068 (mmt) cc_final: 0.5346 (mmm) REVERT: F2 41 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5304 (t70) REVERT: F2 90 SER cc_start: 0.8767 (t) cc_final: 0.8505 (t) REVERT: F2 107 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: G2 41 ASP cc_start: 0.5694 (OUTLIER) cc_final: 0.5322 (t70) REVERT: G2 90 SER cc_start: 0.8910 (t) cc_final: 0.8674 (t) REVERT: H2 15 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: H2 28 ASN cc_start: 0.7902 (t0) cc_final: 0.7388 (t0) REVERT: H2 41 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.5522 (t70) REVERT: H2 61 TYR cc_start: 0.8736 (t80) cc_final: 0.8531 (t80) REVERT: H2 90 SER cc_start: 0.8766 (t) cc_final: 0.8489 (t) REVERT: I2 28 ASN cc_start: 0.7928 (t0) cc_final: 0.7451 (t0) REVERT: I2 41 ASP cc_start: 0.5601 (OUTLIER) cc_final: 0.5286 (t70) REVERT: I2 90 SER cc_start: 0.8698 (t) cc_final: 0.8411 (t) REVERT: J2 15 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: J2 41 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5694 (t70) REVERT: J2 90 SER cc_start: 0.8904 (t) cc_final: 0.8660 (t) REVERT: K2 28 ASN cc_start: 0.7878 (t0) cc_final: 0.7355 (t0) REVERT: K2 41 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5600 (t70) REVERT: K2 90 SER cc_start: 0.8637 (t) cc_final: 0.8376 (t) REVERT: K2 107 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7653 (ptp) REVERT: L2 15 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: L2 28 ASN cc_start: 0.8150 (t0) cc_final: 0.7576 (t0) REVERT: L2 41 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5234 (t70) REVERT: L2 90 SER cc_start: 0.8666 (t) cc_final: 0.8391 (t) outliers start: 242 outliers final: 188 residues processed: 1454 average time/residue: 0.5371 time to fit residues: 1324.0311 Evaluate side-chains 1485 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1268 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 78 LYS Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 153 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 78 LYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 78 LYS Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 24 ASN Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 78 LYS Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain E1 residue 24 ASN Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 157 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 24 ASN Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain H1 residue 371 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 246 LEU Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 182 GLU Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 84 VAL Chi-restraints excluded: chain A2 residue 88 THR Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 88 THR Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 84 VAL Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 5 ASP Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 88 THR Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 64 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 19 VAL Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain I2 residue 88 THR Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain I2 residue 107 MET Chi-restraints excluded: chain I2 residue 113 MET Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 80 SER Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 64 ASP Chi-restraints excluded: chain K2 residue 80 SER Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain K2 residue 107 MET Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 332 optimal weight: 1.9990 chunk 535 optimal weight: 0.0980 chunk 326 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 372 optimal weight: 2.9990 chunk 561 optimal weight: 0.7980 chunk 517 optimal weight: 2.9990 chunk 447 optimal weight: 0.8980 chunk 46 optimal weight: 0.0020 chunk 345 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 58 ASN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 46356 Z= 0.212 Angle : 0.729 15.814 62520 Z= 0.356 Chirality : 0.044 0.383 6876 Planarity : 0.004 0.052 8064 Dihedral : 5.181 25.891 6336 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.50 % Allowed : 27.20 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5676 helix: 0.10 (0.10), residues: 2520 sheet: 0.45 (0.32), residues: 312 loop : -1.73 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPI2 92 HIS 0.003 0.001 HISE2 53 PHE 0.028 0.001 PHEJ1 190 TYR 0.032 0.002 TYRJ1 217 ARG 0.008 0.000 ARGB2 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11352 Ramachandran restraints generated. 5676 Oldfield, 0 Emsley, 5676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1319 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A1 98 PHE cc_start: 0.8546 (p90) cc_final: 0.8263 (p90) REVERT: A1 166 MET cc_start: 0.7803 (mtm) cc_final: 0.7344 (mtt) REVERT: A1 180 MET cc_start: 0.8013 (tpp) cc_final: 0.7356 (tpp) REVERT: A1 197 GLN cc_start: 0.8544 (tt0) cc_final: 0.8318 (tt0) REVERT: B1 21 MET cc_start: 0.8262 (tpp) cc_final: 0.7736 (mmt) REVERT: B1 36 MET cc_start: 0.7796 (ttm) cc_final: 0.7526 (ttm) REVERT: B1 39 MET cc_start: 0.9277 (mtt) cc_final: 0.8918 (mtp) REVERT: B1 116 LEU cc_start: 0.8337 (mt) cc_final: 0.8013 (pp) REVERT: B1 175 TYR cc_start: 0.7569 (m-80) cc_final: 0.7317 (m-80) REVERT: B1 217 TYR cc_start: 0.8257 (t80) cc_final: 0.7156 (t80) REVERT: B1 269 ASN cc_start: 0.7984 (t0) cc_final: 0.7699 (t0) REVERT: B1 301 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7322 (mp0) REVERT: C1 25 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7361 (ptm-80) REVERT: C1 45 MET cc_start: 0.8190 (mmm) cc_final: 0.7568 (tpp) REVERT: C1 76 LEU cc_start: 0.8619 (pt) cc_final: 0.8369 (pp) REVERT: C1 82 ASN cc_start: 0.8364 (m-40) cc_final: 0.7965 (m110) REVERT: C1 180 MET cc_start: 0.7908 (tpp) cc_final: 0.7501 (tpp) REVERT: C1 182 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8428 (mm-30) REVERT: D1 36 MET cc_start: 0.7826 (mtm) cc_final: 0.7536 (ttm) REVERT: D1 45 MET cc_start: 0.8092 (mmm) cc_final: 0.7419 (tpp) REVERT: D1 122 PHE cc_start: 0.8599 (m-80) cc_final: 0.8314 (m-80) REVERT: D1 182 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8191 (mp0) REVERT: D1 197 GLN cc_start: 0.8531 (tt0) cc_final: 0.8291 (tt0) REVERT: D1 269 ASN cc_start: 0.8034 (t0) cc_final: 0.7709 (t0) REVERT: D1 301 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7148 (mp0) REVERT: D1 326 GLU cc_start: 0.8160 (pp20) cc_final: 0.7709 (pp20) REVERT: D1 373 ASP cc_start: 0.6990 (t0) cc_final: 0.6712 (t0) REVERT: E1 25 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7308 (ptm-80) REVERT: E1 166 MET cc_start: 0.7486 (mtm) cc_final: 0.7066 (mtt) REVERT: E1 171 GLU cc_start: 0.8213 (pt0) cc_final: 0.7745 (pt0) REVERT: E1 182 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7815 (mp0) REVERT: E1 197 GLN cc_start: 0.8529 (tt0) cc_final: 0.8227 (tt0) REVERT: E1 274 ARG cc_start: 0.8567 (tpp80) cc_final: 0.7901 (tpp80) REVERT: E1 316 TYR cc_start: 0.8550 (m-10) cc_final: 0.8191 (m-10) REVERT: F1 25 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7340 (ptt90) REVERT: F1 128 LYS cc_start: 0.7040 (ttmt) cc_final: 0.6561 (mmtt) REVERT: F1 269 ASN cc_start: 0.8033 (t0) cc_final: 0.7685 (t0) REVERT: F1 316 TYR cc_start: 0.8598 (m-80) cc_final: 0.8187 (m-10) REVERT: G1 45 MET cc_start: 0.8277 (mmm) cc_final: 0.7764 (tpp) REVERT: G1 77 SER cc_start: 0.8869 (p) cc_final: 0.8624 (p) REVERT: G1 82 ASN cc_start: 0.7946 (m-40) cc_final: 0.7471 (m110) REVERT: G1 171 GLU cc_start: 0.8303 (pt0) cc_final: 0.7863 (pt0) REVERT: G1 180 MET cc_start: 0.8086 (tpp) cc_final: 0.7723 (tpp) REVERT: G1 326 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7804 (pp20) REVERT: H1 45 MET cc_start: 0.8233 (mmm) cc_final: 0.7727 (ttm) REVERT: H1 76 LEU cc_start: 0.8375 (pt) cc_final: 0.8120 (pp) REVERT: H1 77 SER cc_start: 0.8782 (p) cc_final: 0.8378 (p) REVERT: H1 187 TYR cc_start: 0.8430 (t80) cc_final: 0.8030 (t80) REVERT: H1 197 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: H1 273 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7572 (mmm-85) REVERT: H1 316 TYR cc_start: 0.8781 (m-80) cc_final: 0.8416 (m-10) REVERT: I1 25 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7295 (ptm-80) REVERT: I1 45 MET cc_start: 0.8345 (mmm) cc_final: 0.7797 (ttm) REVERT: I1 88 LEU cc_start: 0.8908 (mp) cc_final: 0.8643 (mp) REVERT: I1 166 MET cc_start: 0.7765 (mtm) cc_final: 0.7259 (mtt) REVERT: I1 175 TYR cc_start: 0.7691 (m-80) cc_final: 0.7451 (m-80) REVERT: I1 328 PHE cc_start: 0.8209 (m-10) cc_final: 0.7950 (m-80) REVERT: J1 39 MET cc_start: 0.8997 (mtt) cc_final: 0.8640 (mtp) REVERT: J1 77 SER cc_start: 0.8870 (p) cc_final: 0.8656 (p) REVERT: J1 87 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8050 (tpp) REVERT: J1 166 MET cc_start: 0.7776 (mtm) cc_final: 0.7394 (mtt) REVERT: J1 180 MET cc_start: 0.8460 (tpp) cc_final: 0.7881 (tpp) REVERT: J1 274 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7676 (tpp80) REVERT: K1 21 MET cc_start: 0.8407 (mmt) cc_final: 0.7821 (mmt) REVERT: K1 45 MET cc_start: 0.8349 (tpp) cc_final: 0.7958 (mtt) REVERT: K1 76 LEU cc_start: 0.8605 (pt) cc_final: 0.7883 (pp) REVERT: K1 253 GLU cc_start: 0.7871 (tt0) cc_final: 0.7649 (tt0) REVERT: K1 274 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7557 (tpp80) REVERT: K1 326 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7811 (pp20) REVERT: L1 73 LYS cc_start: 0.7815 (tttp) cc_final: 0.7611 (ttmm) REVERT: L1 182 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: L1 197 GLN cc_start: 0.8592 (tt0) cc_final: 0.8378 (tt0) REVERT: L1 326 GLU cc_start: 0.7854 (pp20) cc_final: 0.7615 (pp20) REVERT: A2 1 MET cc_start: 0.5662 (mmt) cc_final: 0.5144 (mmm) REVERT: A2 15 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: A2 41 ASP cc_start: 0.5454 (OUTLIER) cc_final: 0.5114 (t70) REVERT: A2 90 SER cc_start: 0.8668 (t) cc_final: 0.8414 (t) REVERT: A2 107 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7675 (mtp) REVERT: B2 15 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: B2 28 ASN cc_start: 0.7727 (t0) cc_final: 0.7250 (t0) REVERT: B2 41 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5411 (t70) REVERT: B2 61 TYR cc_start: 0.8773 (t80) cc_final: 0.8543 (t80) REVERT: B2 90 SER cc_start: 0.8712 (t) cc_final: 0.8451 (t) REVERT: C2 15 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: C2 28 ASN cc_start: 0.7796 (t0) cc_final: 0.7285 (t0) REVERT: C2 41 ASP cc_start: 0.5754 (OUTLIER) cc_final: 0.5421 (t70) REVERT: C2 90 SER cc_start: 0.8670 (t) cc_final: 0.8414 (t) REVERT: C2 107 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: D2 15 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: D2 34 TYR cc_start: 0.8618 (t80) cc_final: 0.8377 (t80) REVERT: D2 41 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5349 (t70) REVERT: D2 61 TYR cc_start: 0.8730 (t80) cc_final: 0.8447 (t80) REVERT: D2 90 SER cc_start: 0.8649 (t) cc_final: 0.8376 (t) REVERT: E2 15 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: E2 28 ASN cc_start: 0.7564 (t0) cc_final: 0.7042 (t0) REVERT: E2 41 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.5475 (t70) REVERT: E2 61 TYR cc_start: 0.8779 (t80) cc_final: 0.8543 (t80) REVERT: E2 90 SER cc_start: 0.8671 (t) cc_final: 0.8415 (t) REVERT: E2 107 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7578 (mtp) REVERT: F2 1 MET cc_start: 0.5976 (mmt) cc_final: 0.5267 (mmm) REVERT: F2 41 ASP cc_start: 0.5679 (OUTLIER) cc_final: 0.5319 (t70) REVERT: F2 90 SER cc_start: 0.8683 (t) cc_final: 0.8406 (t) REVERT: F2 107 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7496 (mtp) REVERT: G2 28 ASN cc_start: 0.7576 (t0) cc_final: 0.7032 (t0) REVERT: G2 41 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5358 (t70) REVERT: G2 90 SER cc_start: 0.8924 (t) cc_final: 0.8691 (t) REVERT: H2 15 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: H2 28 ASN cc_start: 0.7799 (t0) cc_final: 0.7319 (t0) REVERT: H2 41 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5507 (t70) REVERT: H2 90 SER cc_start: 0.8711 (t) cc_final: 0.8413 (t) REVERT: H2 107 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7780 (ptp) REVERT: I2 28 ASN cc_start: 0.7837 (t0) cc_final: 0.7401 (t0) REVERT: I2 41 ASP cc_start: 0.5554 (OUTLIER) cc_final: 0.5229 (t70) REVERT: I2 90 SER cc_start: 0.8595 (t) cc_final: 0.8325 (t) REVERT: I2 113 MET cc_start: 0.8279 (ttp) cc_final: 0.7902 (ptm) REVERT: J2 15 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: J2 41 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5560 (t70) REVERT: J2 90 SER cc_start: 0.8882 (t) cc_final: 0.8638 (t) REVERT: K2 28 ASN cc_start: 0.7824 (t0) cc_final: 0.7334 (t0) REVERT: K2 41 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5556 (t70) REVERT: K2 90 SER cc_start: 0.8560 (t) cc_final: 0.8302 (t) REVERT: K2 107 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7690 (ptp) REVERT: L2 15 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: L2 28 ASN cc_start: 0.8108 (t0) cc_final: 0.7517 (t0) REVERT: L2 41 ASP cc_start: 0.5541 (OUTLIER) cc_final: 0.5196 (t70) REVERT: L2 90 SER cc_start: 0.8618 (t) cc_final: 0.8341 (t) outliers start: 225 outliers final: 182 residues processed: 1456 average time/residue: 0.5233 time to fit residues: 1293.2589 Evaluate side-chains 1504 residues out of total 5004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1292 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 24 ASN Chi-restraints excluded: chain A1 residue 60 THR Chi-restraints excluded: chain A1 residue 71 ILE Chi-restraints excluded: chain A1 residue 78 LYS Chi-restraints excluded: chain A1 residue 126 ILE Chi-restraints excluded: chain A1 residue 140 ARG Chi-restraints excluded: chain A1 residue 149 ILE Chi-restraints excluded: chain A1 residue 153 THR Chi-restraints excluded: chain A1 residue 156 TRP Chi-restraints excluded: chain A1 residue 163 THR Chi-restraints excluded: chain A1 residue 242 ILE Chi-restraints excluded: chain A1 residue 255 SER Chi-restraints excluded: chain A1 residue 287 ILE Chi-restraints excluded: chain B1 residue 24 ASN Chi-restraints excluded: chain B1 residue 60 THR Chi-restraints excluded: chain B1 residue 78 LYS Chi-restraints excluded: chain B1 residue 126 ILE Chi-restraints excluded: chain B1 residue 149 ILE Chi-restraints excluded: chain B1 residue 156 TRP Chi-restraints excluded: chain B1 residue 242 ILE Chi-restraints excluded: chain B1 residue 277 MET Chi-restraints excluded: chain B1 residue 287 ILE Chi-restraints excluded: chain C1 residue 60 THR Chi-restraints excluded: chain C1 residue 126 ILE Chi-restraints excluded: chain C1 residue 140 ARG Chi-restraints excluded: chain C1 residue 149 ILE Chi-restraints excluded: chain C1 residue 156 TRP Chi-restraints excluded: chain C1 residue 157 THR Chi-restraints excluded: chain C1 residue 163 THR Chi-restraints excluded: chain C1 residue 209 THR Chi-restraints excluded: chain C1 residue 242 ILE Chi-restraints excluded: chain C1 residue 287 ILE Chi-restraints excluded: chain D1 residue 24 ASN Chi-restraints excluded: chain D1 residue 32 SER Chi-restraints excluded: chain D1 residue 60 THR Chi-restraints excluded: chain D1 residue 78 LYS Chi-restraints excluded: chain D1 residue 94 VAL Chi-restraints excluded: chain D1 residue 149 ILE Chi-restraints excluded: chain D1 residue 156 TRP Chi-restraints excluded: chain D1 residue 174 ASP Chi-restraints excluded: chain D1 residue 242 ILE Chi-restraints excluded: chain D1 residue 287 ILE Chi-restraints excluded: chain E1 residue 60 THR Chi-restraints excluded: chain E1 residue 94 VAL Chi-restraints excluded: chain E1 residue 140 ARG Chi-restraints excluded: chain E1 residue 149 ILE Chi-restraints excluded: chain E1 residue 156 TRP Chi-restraints excluded: chain E1 residue 174 ASP Chi-restraints excluded: chain E1 residue 242 ILE Chi-restraints excluded: chain E1 residue 287 ILE Chi-restraints excluded: chain F1 residue 60 THR Chi-restraints excluded: chain F1 residue 117 LEU Chi-restraints excluded: chain F1 residue 149 ILE Chi-restraints excluded: chain F1 residue 157 THR Chi-restraints excluded: chain F1 residue 197 GLN Chi-restraints excluded: chain F1 residue 242 ILE Chi-restraints excluded: chain F1 residue 287 ILE Chi-restraints excluded: chain G1 residue 60 THR Chi-restraints excluded: chain G1 residue 87 MET Chi-restraints excluded: chain G1 residue 117 LEU Chi-restraints excluded: chain G1 residue 149 ILE Chi-restraints excluded: chain G1 residue 197 GLN Chi-restraints excluded: chain G1 residue 242 ILE Chi-restraints excluded: chain G1 residue 287 ILE Chi-restraints excluded: chain H1 residue 24 ASN Chi-restraints excluded: chain H1 residue 60 THR Chi-restraints excluded: chain H1 residue 78 LYS Chi-restraints excluded: chain H1 residue 87 MET Chi-restraints excluded: chain H1 residue 117 LEU Chi-restraints excluded: chain H1 residue 126 ILE Chi-restraints excluded: chain H1 residue 149 ILE Chi-restraints excluded: chain H1 residue 156 TRP Chi-restraints excluded: chain H1 residue 197 GLN Chi-restraints excluded: chain H1 residue 209 THR Chi-restraints excluded: chain H1 residue 242 ILE Chi-restraints excluded: chain H1 residue 287 ILE Chi-restraints excluded: chain H1 residue 321 LEU Chi-restraints excluded: chain I1 residue 24 ASN Chi-restraints excluded: chain I1 residue 60 THR Chi-restraints excluded: chain I1 residue 76 LEU Chi-restraints excluded: chain I1 residue 117 LEU Chi-restraints excluded: chain I1 residue 126 ILE Chi-restraints excluded: chain I1 residue 140 ARG Chi-restraints excluded: chain I1 residue 149 ILE Chi-restraints excluded: chain I1 residue 156 TRP Chi-restraints excluded: chain I1 residue 163 THR Chi-restraints excluded: chain I1 residue 170 ASN Chi-restraints excluded: chain I1 residue 230 ILE Chi-restraints excluded: chain I1 residue 246 LEU Chi-restraints excluded: chain I1 residue 287 ILE Chi-restraints excluded: chain J1 residue 24 ASN Chi-restraints excluded: chain J1 residue 60 THR Chi-restraints excluded: chain J1 residue 87 MET Chi-restraints excluded: chain J1 residue 117 LEU Chi-restraints excluded: chain J1 residue 126 ILE Chi-restraints excluded: chain J1 residue 140 ARG Chi-restraints excluded: chain J1 residue 149 ILE Chi-restraints excluded: chain J1 residue 156 TRP Chi-restraints excluded: chain J1 residue 163 THR Chi-restraints excluded: chain J1 residue 197 GLN Chi-restraints excluded: chain J1 residue 209 THR Chi-restraints excluded: chain J1 residue 242 ILE Chi-restraints excluded: chain J1 residue 287 ILE Chi-restraints excluded: chain K1 residue 24 ASN Chi-restraints excluded: chain K1 residue 60 THR Chi-restraints excluded: chain K1 residue 78 LYS Chi-restraints excluded: chain K1 residue 87 MET Chi-restraints excluded: chain K1 residue 117 LEU Chi-restraints excluded: chain K1 residue 140 ARG Chi-restraints excluded: chain K1 residue 149 ILE Chi-restraints excluded: chain K1 residue 156 TRP Chi-restraints excluded: chain K1 residue 209 THR Chi-restraints excluded: chain K1 residue 242 ILE Chi-restraints excluded: chain K1 residue 287 ILE Chi-restraints excluded: chain K1 residue 326 GLU Chi-restraints excluded: chain L1 residue 60 THR Chi-restraints excluded: chain L1 residue 71 ILE Chi-restraints excluded: chain L1 residue 78 LYS Chi-restraints excluded: chain L1 residue 126 ILE Chi-restraints excluded: chain L1 residue 140 ARG Chi-restraints excluded: chain L1 residue 156 TRP Chi-restraints excluded: chain L1 residue 159 VAL Chi-restraints excluded: chain L1 residue 182 GLU Chi-restraints excluded: chain L1 residue 209 THR Chi-restraints excluded: chain L1 residue 242 ILE Chi-restraints excluded: chain L1 residue 287 ILE Chi-restraints excluded: chain L1 residue 321 LEU Chi-restraints excluded: chain A2 residue 15 ASP Chi-restraints excluded: chain A2 residue 41 ASP Chi-restraints excluded: chain A2 residue 64 ASP Chi-restraints excluded: chain A2 residue 80 SER Chi-restraints excluded: chain A2 residue 84 VAL Chi-restraints excluded: chain A2 residue 98 SER Chi-restraints excluded: chain A2 residue 107 MET Chi-restraints excluded: chain B2 residue 15 ASP Chi-restraints excluded: chain B2 residue 41 ASP Chi-restraints excluded: chain B2 residue 80 SER Chi-restraints excluded: chain B2 residue 84 VAL Chi-restraints excluded: chain B2 residue 91 ASP Chi-restraints excluded: chain B2 residue 98 SER Chi-restraints excluded: chain C2 residue 5 ASP Chi-restraints excluded: chain C2 residue 13 ASN Chi-restraints excluded: chain C2 residue 15 ASP Chi-restraints excluded: chain C2 residue 41 ASP Chi-restraints excluded: chain C2 residue 64 ASP Chi-restraints excluded: chain C2 residue 80 SER Chi-restraints excluded: chain C2 residue 84 VAL Chi-restraints excluded: chain C2 residue 91 ASP Chi-restraints excluded: chain C2 residue 98 SER Chi-restraints excluded: chain C2 residue 107 MET Chi-restraints excluded: chain D2 residue 15 ASP Chi-restraints excluded: chain D2 residue 41 ASP Chi-restraints excluded: chain D2 residue 64 ASP Chi-restraints excluded: chain D2 residue 80 SER Chi-restraints excluded: chain D2 residue 91 ASP Chi-restraints excluded: chain D2 residue 98 SER Chi-restraints excluded: chain E2 residue 15 ASP Chi-restraints excluded: chain E2 residue 41 ASP Chi-restraints excluded: chain E2 residue 80 SER Chi-restraints excluded: chain E2 residue 84 VAL Chi-restraints excluded: chain E2 residue 91 ASP Chi-restraints excluded: chain E2 residue 98 SER Chi-restraints excluded: chain E2 residue 107 MET Chi-restraints excluded: chain F2 residue 5 ASP Chi-restraints excluded: chain F2 residue 41 ASP Chi-restraints excluded: chain F2 residue 64 ASP Chi-restraints excluded: chain F2 residue 84 VAL Chi-restraints excluded: chain F2 residue 91 ASP Chi-restraints excluded: chain F2 residue 98 SER Chi-restraints excluded: chain F2 residue 107 MET Chi-restraints excluded: chain G2 residue 30 TYR Chi-restraints excluded: chain G2 residue 41 ASP Chi-restraints excluded: chain G2 residue 64 ASP Chi-restraints excluded: chain G2 residue 80 SER Chi-restraints excluded: chain G2 residue 84 VAL Chi-restraints excluded: chain G2 residue 91 ASP Chi-restraints excluded: chain H2 residue 13 ASN Chi-restraints excluded: chain H2 residue 15 ASP Chi-restraints excluded: chain H2 residue 41 ASP Chi-restraints excluded: chain H2 residue 79 VAL Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 91 ASP Chi-restraints excluded: chain H2 residue 98 SER Chi-restraints excluded: chain H2 residue 107 MET Chi-restraints excluded: chain I2 residue 5 ASP Chi-restraints excluded: chain I2 residue 19 VAL Chi-restraints excluded: chain I2 residue 41 ASP Chi-restraints excluded: chain I2 residue 84 VAL Chi-restraints excluded: chain I2 residue 91 ASP Chi-restraints excluded: chain I2 residue 98 SER Chi-restraints excluded: chain J2 residue 15 ASP Chi-restraints excluded: chain J2 residue 41 ASP Chi-restraints excluded: chain J2 residue 64 ASP Chi-restraints excluded: chain J2 residue 84 VAL Chi-restraints excluded: chain J2 residue 91 ASP Chi-restraints excluded: chain J2 residue 98 SER Chi-restraints excluded: chain K2 residue 41 ASP Chi-restraints excluded: chain K2 residue 84 VAL Chi-restraints excluded: chain K2 residue 91 ASP Chi-restraints excluded: chain K2 residue 98 SER Chi-restraints excluded: chain K2 residue 107 MET Chi-restraints excluded: chain L2 residue 5 ASP Chi-restraints excluded: chain L2 residue 15 ASP Chi-restraints excluded: chain L2 residue 41 ASP Chi-restraints excluded: chain L2 residue 64 ASP Chi-restraints excluded: chain L2 residue 79 VAL Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 84 VAL Chi-restraints excluded: chain L2 residue 91 ASP Chi-restraints excluded: chain L2 residue 98 SER Chi-restraints excluded: chain L2 residue 107 MET Chi-restraints excluded: chain L2 residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 564 random chunks: chunk 355 optimal weight: 1.9990 chunk 476 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 412 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 448 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 460 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1 82 ASN ** H1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 82 ASN ** J1 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 82 ASN ** L1 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 112 ASN ** K2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.165522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126761 restraints weight = 63522.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130911 restraints weight = 29545.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.133460 restraints weight = 17240.140| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 46356 Z= 0.227 Angle : 0.744 15.992 62520 Z= 0.362 Chirality : 0.045 0.377 6876 Planarity : 0.004 0.051 8064 Dihedral : 5.171 25.650 6336 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.62 % Allowed : 27.42 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5676 helix: 0.10 (0.10), residues: 2520 sheet: 0.46 (0.32), residues: 312 loop : -1.75 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPH2 92 HIS 0.004 0.001 HISC2 53 PHE 0.026 0.001 PHEJ1 190 TYR 0.041 0.002 TYRG1 217 ARG 0.008 0.000 ARGB2 100 =============================================================================== Job complete usr+sys time: 17920.71 seconds wall clock time: 321 minutes 11.77 seconds (19271.77 seconds total)